scholarly journals Physicochemical Features and Peculiarities of Interaction of AMP with the Membrane

2021 ◽  
Vol 14 (5) ◽  
pp. 471
Author(s):  
Malak Pirtskhalava ◽  
Boris Vishnepolsky ◽  
Maya Grigolava ◽  
Grigol Managadze
Keyword(s):  
Amino Acid ◽  
Antimicrobial Peptides ◽  
Rational Design ◽  
De Novo ◽  
Cell Envelope ◽  
Biological Membrane ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Comprehensive Understanding ◽  
Physicochemical Features

Antimicrobial peptides (AMPs) are anti-infectives that have the potential to be used as a novel and untapped class of biotherapeutics. Modes of action of antimicrobial peptides include interaction with the cell envelope (cell wall, outer- and inner-membrane). A comprehensive understanding of the peculiarities of interaction of antimicrobial peptides with the cell envelope is necessary to perform a rational design of new biotherapeutics, against which working out resistance is hard for microbes. In order to enable de novo design with low cost and high throughput, in silico predictive models have to be invoked. To develop an efficient predictive model, a comprehensive understanding of the sequence-to-function relationship is required. This knowledge will allow us to encode amino acid sequences expressively and to adequately choose the accurate AMP classifier. A shared protective layer of microbial cells is the inner, plasmatic membrane. The interaction of AMP with a biological membrane (native and/or artificial) has been comprehensively studied. We provide a review of mechanisms and results of interactions of AMP with the cell membrane, relying on the survey of physicochemical, aggregative, and structural features of AMPs. The potency and mechanism of AMP action are presented in terms of amino acid compositions and distributions of the polar and apolar residues along the chain, that is, in terms of the physicochemical features of peptides such as hydrophobicity, hydrophilicity, and amphiphilicity. The survey of current data highlights topics that should be taken into account to come up with a comprehensive explanation of the mechanisms of action of AMP and to uncover the physicochemical faces of peptides, essential to perform their function. Many different approaches have been used to classify AMPs, including machine learning. The survey of knowledge on sequences, structures, and modes of actions of AMP allows concluding that only possessing comprehensive information on physicochemical features of AMPs enables us to develop accurate classifiers and create effective methods of prediction. Consequently, this knowledge is necessary for the development of design tools for peptide-based antibiotics.

scholarly journals The Possibility of Common Amino Acid Sequences in High-Sulphur Protein Fractions from Wool

1969 ◽  
Vol 22 (5) ◽  
pp. 1197 ◽  
Author(s):  
RL Darskus ◽  
JM Gillespie ◽  
H Lindley
Keyword(s):  
Amino Acid ◽  
High Voltage ◽  
Paper Electrophoresis ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Protein Fractions ◽  
Common Amino Acid ◽  
Amino Acid Compositions ◽  
Merino Wool ◽  
Derivatives Of

S-Carboxymethyl derivatives of the high-sulphur components of reduced Merino wool have been subdivided by chromatography into 17 fractions, the amino acid compositions of which are reported. Tryptic, chymotryptic, and thermolysin digests of each fraction have been studied by high-voltage paper electrophoresis at pH 3�5 and 6�5. The results suggest that the high-sulphur proteins consist of families of proteins probably containing common structural features. Evidence is presented that the heterogeneity of high-sulphur proteins is not artefactual.

scholarly journals Evolutionary Algorithms for Improving De Novo Peptide Sequencing

2021 ◽  
Author(s):  
◽  
Samaneh Azari
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Peptide Identification ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Multi Objective ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

<p>De novo peptide sequencing algorithms have been developed for peptide identification in proteomics from tandem mass spectra (MS/MS), which can be used to identify and discover novel peptides and proteins that do not have a database available. Despite improvements in MS instrumentation and de novo sequencing methods, a significant number of CID MS/MS spectra still remain unassigned with the current algorithms, often leading to low confidence of peptide assignments to the spectra. Moreover, current algorithms often fail to construct the completely matched sequences, and produce partial matches. Therefore, identification of full-length peptides remains challenging. Another major challenge is the existence of noise in MS/MS spectra which makes the data highly imbalanced. Also missing peaks, caused by incomplete MS fragmentation makes it more difficult to infer a full-length peptide sequence. In addition, the large search space of all possible amino acid sequences for each spectrum leads to a high false discovery rate. This thesis focuses on improving the performance of current methods by developing new algorithms corresponding to three steps of preprocessing, sequence optimisation and post-processing using machine learning for more comprehensive interrogation of MS/MS datasets. From the machine learning point of view, the three steps can be addressed by solving different tasks such as classification, optimisation, and symbolic regression. Since Evolutionary Algorithms (EAs), as effective global search techniques, have shown promising results in solving these problems, this thesis investigates the capability of EAs in improving the de novo peptide sequencing. In the preprocessing step, this thesis proposes an effective GP-based method for classification of signal and noise peaks in highly imbalanced MS/MS spectra with the purpose of having a positive influence on the reliability of the peptide identification. The results show that the proposed algorithm is the most stable classification method across various noise ratios, outperforming six other benchmark classification algorithms. The experimental results show a significant improvement in high confidence peptide assignments to MS/MS spectra when the data is preprocessed by the proposed GP method. Moreover, the first multi-objective GP approach for classification of peaks in MS/MS data, aiming at maximising the accuracy of the minority class (signal peaks) and the accuracy of the majority class (noise peaks) is also proposed in this thesis. The results show that the multi-objective GP method outperforms the single objective GP algorithm and a popular multi-objective approach in terms of retaining more signal peaks and removing more noise peaks. The multi-objective GP approach significantly improved the reliability of peptide identification. This thesis proposes a GA-based method to solve the complex optimisation task of de novo peptide sequencing, aiming at constructing full-length sequences. The proposed GA method benefits the GA capability of searching a large search space of potential amino acid sequences to find the most likely full-length sequence. The experimental results show that the proposed method outperforms the most commonly used de novo sequencing method at both amino acid level and peptide level. This thesis also proposes a novel method for re-scoring and re-ranking the peptide spectrum matches (PSMs) from the result of de novo peptide sequencing, aiming at minimising the false discovery rate as a post-processing approach. The proposed GP method evolves the computer programs to perform regression and classification simultaneously in order to generate an effective scoring function for finding the correct PSMs from many incorrect ones. The results show that the new GP-based PSM scoring function significantly improves the identification of full-length peptides when it is used to post-process the de novo sequencing results.</p>

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

2011 ◽  
Vol 6 (4) ◽  
pp. 545-557 ◽  
Author(s):  
Malay Choudhury ◽  
Takahiro Oku ◽  
Shoji Yamada ◽  
Masaharu Komatsu ◽  
Keita Kudoh ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Consensus Sequence ◽  
Structural Features ◽  
Lipid Binding ◽  
Japanese Eel ◽  
Amino Acid Sequences ◽  
Novel Genes ◽  
Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Expression of intermediate filament proteins during development of Xenopus laevis. I. cDNA clones encoding different forms of vimentin

Development ◽  
1989 ◽  
Vol 105 (2) ◽  
pp. 279-298
Author(s):  
H. Herrmann ◽  
B. Fouquet ◽  
W.W. Franke
Keyword(s):  
Amino Acid ◽  
Xenopus Laevis ◽  
Intermediate Filament ◽  
De Novo ◽  
Mesenchymal Cell ◽  
Amino Acid Sequences ◽  
Cytoskeletal Proteins ◽  
Cdna Clones ◽  
Mammalian Development ◽  
Intermediate Filament Proteins

To provide a basis for studies of the expression of genes encoding the diverse kinds of intermediate-filament (IF) proteins during embryogenesis of Xenopus laevis we have isolated and characterized IF protein cDNA clones. Here we report the identification of two types of Xenopus vimentin, Vim1 and Vim4, with their complete amino acid sequences as deduced from the cloned cDNAs, both of which are expressed during early embryogenesis. In addition, we have obtained two further vimentin cDNAs (Vim2 and 3) which are sequence variants of closely related Vim1. The high evolutionary conservation of the amino acid sequences (Vim1: 458 residues; Mr approximately 52,800; Vim4: 463 residues; Mr approximately 53,500) to avian and mammalian vimentin and, to a lesser degree, to desmin from the same and higher vertebrate species, is emphasized, including conserved oligopeptide motifs in their head domains. Using these cDNAs in RNA blot and ribonuclease protection assays of various embryonic stages, we observed a dramatic increase of vimentin RNA at stage 14, in agreement with immunocytochemical results obtained with antibody VIM-3B4. The significance of very weak mRNA signals detected in earlier stages is discussed in relation to negative immunocytochemical results obtained in these stages. The first appearance of vimentin has been localized to a distinct mesenchymal cell layer underlying the neural plate or tube, respectively. The results are discussed in relation to programs of de novo synthesis of other cytoskeletal proteins in amphibian and mammalian development.

Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties

2021 ◽  
Vol 77 (5) ◽  
pp. 690-702
Author(s):  
Pandian Ramesh ◽  
Selvarajan Sigamani Sundaresan ◽  
Nagaraj Shobana ◽  
Thangaraj Vinuchakkaravarthy ◽  
Kandasamy Sivakumar ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Crystal Structure Analysis ◽  
Oxygen Molecule ◽  
Amino Acid Sequences ◽  
Physical Parameters ◽  
Oxygen Binding ◽  
Binding Properties ◽  
Form Analysis ◽  
Inverse Transition

Crystal structures of hemoglobin (Hb) from two flightless birds, ostrich (Struthio camelus) and turkey (Meleagris gallopova), were determined. The ostrich Hb structure was solved to a resolution of 2.22 Å, whereas two forms of turkey Hb were solved to resolutions of 1.66 Å (turkey monoclinic structure; TMS) and 1.39 Å (turkey orthorhombic structure; TOS). Comparison of the amino-acid sequences of ostrich and turkey Hb with those from other avian species revealed no difference in the number of charged residues, but variations were observed in the numbers of hydrophobic and polar residues. Amino-acid-composition-based computation of various physical parameters, in particular their lower inverse transition temperatures and higher average hydrophobicities, indicated that the structures of ostrich and turkey Hb are likely to be highly ordered when compared with other avian Hbs. From the crystal structure analysis, the liganded state of ostrich Hb was confirmed by the presence of an oxygen molecule between the Fe atom and the proximal histidine residue in all four heme regions. In turkey Hb (both TMS and TOS), a water molecule was bound instead of an oxygen molecule in all four heme regions, thus confirming that they assumed the aqua-met form. Analysis of tertiary- and quaternary-structural features led to the conclusion that ostrich oxy Hb and turkey aqua-met Hb adopt the R-/RH-state conformation.

scholarly journals Unevolved De Novo Proteins Have Innate Tendencies to Bind Transition Metals

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 8 ◽  
Author(s):  
Michael S. Wang ◽  
Kenric J. Hoegler ◽  
Michael H. Hecht
Keyword(s):  
Amino Acid ◽  
Transition Metals ◽  
Metal Binding ◽  
Combinatorial Library ◽  
De Novo ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Ancestral Sequences ◽  
Wide Range ◽  
Catalytic Functions

Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles. Although these sequences were neither designed nor evolved to bind metals, the majority of them have innate tendencies to bind the transition metals copper, cobalt, and zinc with high nanomolar to low-micromolar affinity.

Subunit II (b') and Not Subunit I (b) of Photosynthetic ATP Synthases is Equivalent to Subunit b of the ATP Synthases from Nonphotosynthetic Eubacteria. Evidence for a New Assignment of b-Type F0 Subunits

1997 ◽  
Vol 52 (11-12) ◽  
pp. 789-798 ◽  
Author(s):  
Hans-Jürgen Tiburzy ◽  
Richard J. Berzborn
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Structural Feature ◽  
Atp Synthase ◽  
Primary Structure ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
E Coli ◽  
Subunit B ◽  
Atp Synthases

Abstract Subunit I of chloroplast ATP synthase is reviewed until now to be equivalent to subunit b of Escherichia coli ATP synthase, whereas subunit II is suggested to be an additional subunit in photosynthetic ATP synthases lacking a counterpart in E. coli. After publication of some sequences of subunits II a revision of this assignment is necessary. Based on the analysis of 51 amino acid sequences of b-type subunits concerning similarities in primary structure, iso­electric point and a discovered discontinuous structural feature, our data provide evidence that chloroplast subunit II (subunit b' of photosynthetic eubacteria) and not chloroplast subunit I (subunit b of photosynthetic eubacteria) is the equivalent of subunit b of nonphoto­ synthetic eubacteria, and therefore does have a counterpart in e.g. E. coli. In consequence, structural features essential for function should be looked for on subunit II (b').

scholarly journals Protein engineering of the 2-haloacid halidohydrolase IVa from Pseudomonas cepacia MBA4

1993 ◽  
Vol 292 (1) ◽  
pp. 69-74 ◽  
Author(s):  
W Asmara ◽  
U Murdiyatmo ◽  
A J Baines ◽  
A T Bull ◽  
D J Hardman
Keyword(s):  
Amino Acid ◽  
Rational Design ◽  
Catalytic Mechanism ◽  
Protonated Form ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Pseudomonas Cepacia ◽  
Amino Acid Residues ◽  
Substrate Complex ◽  
Key Residues

The chemical modification of L-2-haloacid halidohydrolase IVa (Hdl IVa), originally identified in Pseudomonas cepacia MBA4, produced as a recombinant protein in Escherichia coli DH5 alpha, led to the identification of histidine and arginine as amino acid residues likely to play a part in the catalytic mechanism of the enzyme. These results, together with DNA sequence and analyses [Murdiyatmo, Asmara, Baines, Bull and Hardman (1992) Biochem. J. 284, 87-93] provided the basis for the rational design of a series of random- and site-directed-mutagenesis experiments of the Hdl IVa structural gene (hdl IVa). Subsequent apparent kinetic analyses of purified mutant enzymes identified His-20 and Arg-42 as the key residues in the activity of this halidohydrolase. It is also proposed that Asp-18 is implicated in the functioning of the enzyme, possibly by positioning the correct tautomer of His-20 for catalysis in the enzyme-substrate complex and stabilizing the protonated form of His-20 in the transition-state complex. Comparison of conserved amino acid sequences between the Hdl IVa and other halidohydrolases suggests that L-2-haloacid halidohydrolases contain conserved amino acid sequences that are not found in halidohydrolases active towards both D- and L-2-monochloropropionate.

scholarly journals In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

2017 ◽  
Vol 61 (4) ◽  
pp. 421-426 ◽  
Author(s):  
Joanna Kołsut ◽  
Paulina Borówka ◽  
Błażej Marciniak ◽  
Ewelina Wójcik ◽  
Arkadiusz Wojtasik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Virulence Factors ◽  
De Novo ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Common Disease ◽  
Bacterial Genomes ◽  
E Coli

AbstractIntroduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors.Material and Methods: A total of 14 pathogenic for poultry E. coli strains were isolated, and their DNA was sequenced, assembled de novo, and annotated. Amino acid sequences from these bacteria and an additional 16 freely available APEC amino acid sequences were analysed with the DIFFIND tool to define their virulence factors.Results: The DIFFIND tool enabled quick, reliable, and convenient assessment of the differences between compared amino acid sequences from bacterial genomes. The presence of 16 protein sequences indicated as pathogenicity factors in poultry resulted in the generation of a heatmap which categorises genomes in terms of the existence and similarity of the analysed protein sequences.Conclusion: The proposed method of detection of virulence factors using the capabilities of the DIFFIND tool may be useful in the analysis of similarities of E. coli and other sequences deriving from bacteria. Phylogenetic analysis resulted in reliable segregation of 30 APEC strains into five main clusters containing various virulence associated genes (VAGs).

Sign in / Sign up

Export Citation Format

Share Document