scholarly journals Prediction of amyloidogenicity based on the n-gram analysis

2016 ◽  
Author(s):  
Michał Jan Burdukiewicz ◽  
Piotr Sobczyk ◽  
Stefan Rödiger ◽  
Anna Duda-Madej ◽  
Paweł Mackiewicz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Hot Spots ◽  
Permutation Test ◽  
Strongly Correlated ◽  
Amino Acid Residues ◽  
Data Set ◽  
Amyloid Peptides ◽  
External Data ◽  
N Gram

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers, based on data collected in the AmyLoad database. Only the most informative n-grams, selected by our Quick Permutation Test, were considered. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on more general properties of amino acids, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids, which are strongly correlated with hydrophobicity, a tendency to form ß-sheets and rigidity of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were already confirmed experimentally. AmyloGram is available as a web-server: www.smorfland.uni.wroc.pl/amylogram/. The code and results are publicly available at: www.github.com/michbur/prediction_amyloidogenicity_ngram/.

scholarly journals Prediction of amyloidogenicity based on the n-gram analysis

2016 ◽  
Author(s):  
Michał Jan Burdukiewicz ◽  
Piotr Sobczyk ◽  
Stefan Rödiger ◽  
Anna Duda-Madej ◽  
Paweł Mackiewicz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Hot Spots ◽  
Permutation Test ◽  
Strongly Correlated ◽  
Amino Acid Residues ◽  
Data Set ◽  
Amyloid Peptides ◽  
External Data ◽  
N Gram

Amyloids are proteins associated with the number of clinical disorders (e.g., Alzheimer's, Creutzfeldt-Jakob's and Huntington's diseases). Despite their diversity, all amyloid proteins can undergo aggregation initiated by 6- to 15-residue segments, called hot spots. To find the patterns defining the hot-spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers, based on data collected in the AmyLoad database. Only the most informative n-grams, selected by our Quick Permutation Test, were considered. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on more general properties of amino acids, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids, which are strongly correlated with hydrophobicity, a tendency to form ß-sheets and rigidity of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were already confirmed experimentally. AmyloGram is available as a web-server: www.smorfland.uni.wroc.pl/amylogram/. The code and results are publicly available at: www.github.com/michbur/prediction_amyloidogenicity_ngram/.

The C-terminal sequence of amino acid residues of κ-casein isolated from buffalo's milk

1967 ◽  
Vol 34 (1) ◽  
pp. 85-88 ◽  
Author(s):  
M. H. Abd El-Salam ◽  
W. Manson
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Peptide Chain ◽  
Amino Acid Residues ◽  
Terminal Sequence ◽  
Carboxypeptidase A ◽  
Phosphorous Content ◽  
Single Peptide

SummaryWhen κ-casein from buffalo's milk was treated with carboxypeptidase A (EC 3. 4. 2. 1),4 amino acids, valine, threonine, serine and alanine were released from the protein in a manner consistent with the view that they originate in the C-terminal sequence of a single peptide chain. The amounts produced suggest a minimum molecular weight for buffalo κ-casein of approximately 17000, in agreement with the value calculated from the phosphorous content on the basis of the presence of 2 phosphorus atoms/molecule. A comparison is made with the C-terminal sequence reported for bovine κ-casein.

Structural characterization of folded and extended conformations in peptides containing γ amino acids with proteinogenic side chains: crystal structures of γn, (αγ)n and γγδγ sequences

2015 ◽  
Vol 39 (5) ◽  
pp. 3319-3326 ◽  
Author(s):  
Madhusudana M. B. Reddy ◽  
K. Basuroy ◽  
S. Chandrappa ◽  
B. Dinesh ◽  
B. Vasantha ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Crystal Structures ◽  
Structural Characterization ◽  
Side Chains ◽  
Amino Acid Residues

γn amino acid residues can be incorporated into structures in γn and hybrid sequences containing folded and extended α and δ residues.

P–283 Combination between amino acids profile of the spent culture media and morphokinetics parameters of human embryos to determine its viability

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
N Adel ◽  
M Kadah ◽  
S Abdulghafar ◽  
M Elmahdy ◽  
D Ghareeb ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Embryo Development ◽  
Culture Medium ◽  
Essential Amino Acids ◽  
Human Embryos ◽  
Data Set ◽  
Group A ◽  
Amino Acids Profile ◽  
Group D

Abstract Study question How to determine human embryo viability noninvasively before embryo transfer? Summary answer We propose that the combination of the amino acid profile of an individual embryo with its morphokinetics will provide noninvasive tool to determine its viability. What is known already It was already known that human embryos at early cleavage require non-essential amino acids, while at the 8-cell to blastocyst stages, a mixture of non-essential and essential amino acids. Amino acids have important roles during embryo development. Acting as biosynthetic precursors,buffers of intracellular pH in the embryo, antioxidants, energy sources and regulators of metabolic function and signaling pathways. Many studies have used time-lapse to analyze human embryonic development including the process of fertilization and assessment of early events and introducednoninvasive prognostic markers which predict embryo development and correlate it to IVF treatment outcomes. Study design, size, duration This study was a prospective cohort study approved by the Clinical Trial Ethical Committee of Faculty of Medicine, Alexandria University according to ethical standards of scientific research (Serial number: 0303721).Thirty females aged 30.13 ± 4.83 years undergoing ICSI cycle in the Madina Fertility Center, during the period of March 2018 to November 2019.202 MII oocytes were incubated individually in embryoscope. Participants/materials, setting, methods Embryos (n = 161) were divided on Day 5 into two groups –developed embryos “Group D” (embryos that developed to blastocyst) and arrested embryos “Group A” (embryos remain at cleavage stage and fail to develop to blastocys).Developed embryos (Group D) included 99 embryos, and Arrested embryos (Group A) included 62 embryos. For each group, morphokinetic developmental points using embryoscope and the different amino acids concentrations in spent culture medium were analyzed using LC- mass spectro etry. Main results and the role of chance On one hand, the first appearance of pronuclei (TPNa), t2, t4 and CC2 in group D occurred significantly earlier than those of Group A.Analysis of 19 essential and non-essential amino acids in spent culture medium of each embryo in the two studied groups D and A showed a significantly higher concentration of two essential amino acids L-Valine (145.73 ± 150.96) and L-Phenylalanine (61.59 ± 55.78) in Group D than their concentration in Group A ( 104.58 ± 33.58, 44.24 ± 14.61, respectively , p ≤ 0.05).and significantly lower concentration of three non-essential amino acids L-Tyrosine (62.56 ± 41.03) , L-Cysteine (19.48 ± 11.90), and L-Alanine (136.0 ± 389.83) observed in Group D when compared to Group A (69.57 ± 20.78, 22.37 ± 8.59,145.33 ± 165.22, respectively, Limitations, reasons for caution It is important to note, that results were developed on a data set from one clinic with different stimulation protocols, a multicenter data and a correlation with the stimulation protocol used should be involved in future studies, in addition a larger sample size to avoid high standard deviation is recommended Wider implications of the findings: We can conclude that amino acid turnover is independent of the traditional morphological assessment of embryos and it may reflect its viability. The prospective combined use of amino acids profile of individual embryo and its morphokinetic parameters may contribute to introduce a new noninvasivs tool that may improve implantation rate Trial registration number 0303721

scholarly journals SLC6A14, a Pivotal Actor on Cancer Stage: When Function Meets Structure

2019 ◽  
Vol 24 (9) ◽  
pp. 928-938 ◽  
Author(s):  
Luca Palazzolo ◽  
Chiara Paravicini ◽  
Tommaso Laurenzi ◽  
Sara Adobati ◽  
Simona Saporiti ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Amino Acid ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Interactions ◽  
Amino Acid Residues ◽  
Dibasic Amino Acid ◽  
Novel Target ◽  
Function Relationship ◽  
Dynamics Simulations

SLC6A14 (ATB0,+) is a sodium- and chloride-dependent neutral and dibasic amino acid transporter that regulates the distribution of amino acids across cell membranes. The transporter is overexpressed in many human cancers characterized by an increased demand for amino acids; as such, it was recently acknowledged as a novel target for cancer therapy. The knowledge on the molecular mechanism of SLC6A14 transport is still limited, but some elegant studies on related transporters report the involvement of the 12 transmembrane α-helices in the transport mechanism, and describe structural rearrangements mediated by electrostatic interactions with some pivotal gating residues. In the present work, we constructed a SLC6A14 model in outward-facing conformation via homology modeling and used molecular dynamics simulations to predict amino acid residues critical for substrate recognition and translocation. We docked the proteinogenic amino acids and other known substrates in the SLC6A14 binding site to study both gating regions and the exposed residues involved in transport. Interestingly, some of these residues correspond to those previously identified in other LeuT-fold transporters; however, we could also identify a novel relevant residue with such function. For the first time, by combined approaches of molecular docking and molecular dynamics simulations, we highlight the potential role of these residues in neutral amino acid transport. This novel information unravels new aspects of the human SLC6A14 structure–function relationship and may have important outcomes for cancer treatment through the design of novel inhibitors of SLC6A14-mediated transport.

scholarly journals Hyaluronan-binding region of aggrecan from pig laryngeal cartilage. Amino acid sequence, analysis of N-linked oligosaccharides and location of the keratan sulphate

1992 ◽  
Vol 286 (3) ◽  
pp. 761-769 ◽  
Author(s):  
F P Barry ◽  
J U Gaw ◽  
C N Young ◽  
P J Neame
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Signal Peptidase ◽  
Amino Acid Residues ◽  
Terminal Sequence ◽  
Binding Region ◽  
Keratan Sulphate ◽  
Laryngeal Cartilage ◽  
Hyaluronan Binding

The hyaluronan-binding region (HABR) was prepared from pig laryngeal cartilage aggrecan and the amino acid sequence was determined. The HABR had two N-termini: one N-terminal sequence was Val-Glu-Val-Ser-Glu-Pro (367 amino acids in total), and a second N-terminal sequence (Ala-Ile-Ser-Val-Glu-Val; 370 amino acids in total) was found to arise due to alternate cleavage by the signal peptidase. The N-linked oligosaccharides were analysed by examining their reactivity with a series of lectins. It was found that the N-linked oligosaccharide on loop A was of the mannose type, while that on loop B was of the complex type. No reactivity was detected between the N-linked oligosaccharide on loop B' and any of the lectins. The location of keratan sulphate (KS) in the HABR was determined by Edman degradation of the immobilized KS-containing peptide. The released amino acid derivatives were collected and tested for the presence of epitope to antibody 5-D-4. On the basis of 5-D-4 reactivity and sequencing yields, the KS chains are attached to threonine residues 352 and 357. There is no KS at threonine-355. This site is not in fact in G1, but about 16 amino acid residues into the interglobular domain. Comparison of the structure of the KS chain from the HABR and from the KS domain of pig laryngeal cartilage aggrecan was made by separation on polyacrylamide gels of the oligosaccharides arising from digestion with keratanase. Comparison of the oligosaccharide maps suggests that the KS chains from both parts of the aggrecan molecule have the same structure.

ChemInform Abstract: β-Nitro-α-amino Acids as Latent α,β-Dehydro-α-amino Acid Residues in Peptides.

ChemInform ◽  
2010 ◽  
Vol 30 (34) ◽  
pp. no-no
Author(s):  
Phillip A. Coghlan ◽  
Christopher J. Easton
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residues

MAPRes: Mining association patterns among preferred amino acid residues in the vicinity of amino acids targeted for post-translational modifications

PROTEOMICS ◽  
2008 ◽  
Vol 8 (10) ◽  
pp. 1954-1958 ◽  
Author(s):  
Ishtiaq Ahmad ◽  
Wajahat M. Qazi ◽  
Ahmed Khurshid ◽  
Munir Ahmad ◽  
Daniel C. Hoessli ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Residues ◽  
Association Patterns ◽  
Post Translational Modifications

Targeting motifs and functional parameters governing the assembly of connexins into gap junctions

2000 ◽  
Vol 349 (1) ◽  
pp. 281-287 ◽  
Author(s):  
Patricia E. M. MARTIN ◽  
James STEGGLES ◽  
Claire WILSON ◽  
Shoeb AHMAD ◽  
W. Howard EVANS
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Gap Junctions ◽  
Gap Junction ◽  
Mammalian Cells ◽  
Fluorescent Protein ◽  
Lucifer Yellow ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Green Fluorescent

To study the assembly of gap junctions, connexin-green-fluorescent-protein (Cx-GFP) chimeras were expressed in COS-7 and HeLa cells. Cx26- and Cx32-GFP were targeted to gap junctions where they formed functional channels that transferred Lucifer Yellow. A series of Cx32-GFP chimeras, truncated from the C-terminal cytoplasmic tail, were studied to identify amino acid sequences governing targeting from intracellular assembly sites to the gap junction. Extensive truncation of Cx32 resulted in failure to integrate into membranes. Truncation of Cx32 to residue 207, corresponding to removal of most of the 78 amino acids on the cytoplasmic C-terminal tail, led to arrest in the endoplasmic reticulum and incomplete oligomerization. However, truncation to amino acid 219 did not impair Cx oligomerization and connexon hemichannels were targeted to the plasma membrane. It was concluded that a crucial gap-junction targeting sequence resides between amino acid residues 207 and 219 on the cytoplasmic C-terminal tail of Cx32. Studies of a Cx32E208K mutation identified this as one of the key amino acids dictating targeting to the gap junction, although oligomerization of this site-specific mutation into hexameric hemichannels was relatively unimpaired. The studies show that expression of these Cx-GFP constructs in mammalian cells allowed an analysis of amino acid residues involved in gap-junction assembly.

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