Partial tertiary structure assignment for the acetylcholine receptor on the basis of the hydrophobicity of amino acid sequences and channel location using single group rotation theory

1983 ◽  
Vol 111 (3) ◽  
pp. 1022-1026 ◽  
Author(s):  
Edward M. Kosower
Keyword(s):  
Amino Acid ◽  
Acetylcholine Receptor ◽  
Tertiary Structure ◽  
Amino Acid Sequences ◽  
Single Group ◽  
Group Rotation ◽  
Structure Assignment

scholarly journals In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3160 ◽  
Author(s):  
Kumar Manochitra ◽  
Subhash Chandra Parija
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Treatment Modalities ◽  
Bioinformatic Tools ◽  
Complex Protein ◽  
A Cell ◽  
Quaternary Structures

BackgroundAmoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-richEntamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal inE. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential. However, studies in this aspect are scant. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using appropriatein-silicomethods.MethodsThe amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.ResultsThe protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be an extracellular protein, peroxiredoxin a peripheral membrane protein while Gal/GalNAc lectin was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc lectin, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All the three proteins exhibited similarity in their structures and were mostly composed of loops.DiscussionThe structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures of SREHP and peroxiredoxin predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

scholarly journals Analysis of a nucleotide-binding site of 5-lipoxygenase by affinity labelling: binding characteristics and amino acid sequences

2000 ◽  
Vol 351 (3) ◽  
pp. 697-707 ◽  
Author(s):  
Ying-Yi ZHANG ◽  
Tove HAMMARBERG ◽  
Olof RADMARK ◽  
Bengt SAMUELSSON ◽  
Carol F. NG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Tertiary Structure ◽  
Nucleotide Binding ◽  
Peptide Sequencing ◽  
Amino Acid Sequences ◽  
Nucleotide Binding Site ◽  
Atp Binding ◽  
Binding Characteristics ◽  
Atp Binding Site

5-Lipoxygenase (5LO) catalyses the first two steps in the biosynthesis of leukotrienes, which are inflammatory mediators derived from arachidonic acid. 5LO activity is stimulated by ATP; however, a consensus ATP-binding site or nucleotide-binding site has not been found in its protein sequence. In the present study, affinity and photoaffinity labelling of 5LO with 5′-p-fluorosulphonylbenzoyladenosine (FSBA) and 2-azido-ATP showed that 5LO bound to the ATP analogues quantitatively and specifically and that the incorporation of either analogue inhibited ATP stimulation of 5LO activity. The stoichiometry of the labelling was 1.4mol of FSBA/mol of 5LO (of which ATP competed with 1mol/mol) or 0.94mol of 2-azido-ATP/mol of 5LO (of which ATP competed with 0.77mol/mol). Labelling with FSBA prevented further labelling with 2-azido-ATP, indicating that the same binding site was occupied by both analogues. Other nucleotides (ADP, AMP, GTP, CTP and UTP) also competed with 2-azido-ATP labelling, suggesting that the site was a general nucleotide-binding site rather than a strict ATP-binding site. Ca2+, which also stimulates 5LO activity, had no effect on the labelling of the nucleotide-binding site. Digestion with trypsin and peptide sequencing showed that two fragments of 5LO were labelled by 2-azido-ATP. These fragments correspond to residues 73–83 (KYWLNDDWYLK, in single-letter amino acid code) and 193–209 (FMHMFQSSWNDFADFEK) in the 5LO sequence. Trp-75 and Trp-201 in these peptides were modified by the labelling, suggesting that they were immediately adjacent to the C-2 position of the adenine ring of ATP. Given the stoichiometry of the labelling, the two peptide sequences of 5LO were probably near each other in the enzyme's tertiary structure, composing or surrounding the ATP-binding site of 5LO.

Synopses from the poster exhibition organized by I. M. Kerr, 1. Interferon: a tertiary structure predicted from amino acid sequences

1982 ◽  
Vol 299 (1094) ◽  
pp. 125-127 ◽  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
X Ray ◽  
Three Dimensional Structure ◽  
X Ray Crystallography ◽  
Functional Studies

Functional studies on interferon would be helped by a three-dimensional structure for the molecule. However, it may be several years before the structure of the protein is determined by X-ray crystallography. We have therefore used available methods for predicting the secondary - and the tertiary - structure of a protein from its amino acid sequence to propose a tertiary model involving the packing of four a-helices. Details of this work have been published elsewhere (Sternberg & Cohen 1982).

NEAT-FLEX: Predicting the conformational flexibility of amino acids using neuroevolution of augmenting topologies

2017 ◽  
Vol 15 (03) ◽  
pp. 1750009 ◽  
Author(s):  
Bruno Grisci ◽  
Márcio Dorn
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Tertiary Structure ◽  
Structural Information ◽  
Protein Structures ◽  
Three Dimensional ◽  
Conformational Flexibility ◽  
Amino Acid Sequences ◽  
Conformational Search ◽  
Back Propagation Algorithm

The development of computational methods to accurately model three-dimensional protein structures from sequences of amino acid residues is becoming increasingly important to the structural biology field. This paper addresses the challenge of predicting the tertiary structure of a given amino acid sequence, which has been reported to belong to the NP-Complete class of problems. We present a new method, namely NEAT–FLEX, based on NeuroEvolution of Augmenting Topologies (NEAT) to extract structural features from (ABS) proteins that are determined experimentally. The proposed method manipulates structural information from the Protein Data Bank (PDB) and predicts the conformational flexibility (FLEX) of residues of a target amino acid sequence. This information may be used in three-dimensional structure prediction approaches as a way to reduce the conformational search space. The proposed method was tested with 24 different amino acid sequences. Evolving neural networks were compared against a traditional error back-propagation algorithm; results show that the proposed method is a powerful way to extract and represent structural information from protein molecules that are determined experimentally.

Einfluß der Tertiärstruktur auf die serologischen Eigenschaften des Tabakmosaikvirus

1963 ◽  
Vol 18 (12) ◽  
pp. 1015-1021 ◽  
Author(s):  
F. Alfred Anderer ◽  
Dieter Handschuh
Keyword(s):  
Amino Acid ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
Polypeptide Chain ◽  
Amino Acid Sequences ◽  
Virus Protein ◽  
Protein Subunits ◽  
Specific Antibodies ◽  
The Reformation ◽  
Derivatives Of

Four derivatives of tobacco mosaic virus protein have been prepared by substituting different groups of the amino acid sidechains. The influence of the substituents on the reformation of the native protein structure has been studied by electron microscopy (reformation of typical protein rods) and by serological methods (precipitation with anti TMV serum). The results indicate that the reaction with anti TMV serum is not dependent on the correct quaternary structure of the virus, but rather on the tertiary structure of the protein subunits of the virus. There is no evidence for specific antibodies against isolated amino acid sequences of the polypeptide chain of TMV. Further evidence is provided by serological investigations of virus protein partially degradated by enzymes.

POPS: A COMPUTATIONAL TOOL FOR MODELING AND PREDICTING PROTEASE SPECIFICITY

2005 ◽  
Vol 03 (03) ◽  
pp. 551-585 ◽  
Author(s):  
SARAH E. BOYD ◽  
ROBERT N. PIKE ◽  
GEORGE B. RUDY ◽  
JAMES C. WHISSTOCK ◽  
MARIA GARCIA DE LA BANDA
Keyword(s):  
Amino Acid ◽  
Computational Models ◽  
Tertiary Structure ◽  
Expert Knowledge ◽  
Amino Acid Sequences ◽  
Specific Amino Acid ◽  
Cellular Processes ◽  
Test Models ◽  
Novel Method ◽  
Protease Specificity

Proteases play a fundamental role in the control of intra- and extra-cellular processes by binding and cleaving specific amino acid sequences. Identifying these targets is extremely challenging. Current computational attempts to predict cleavage sites are limited, representing these amino acid sequences as patterns or frequency matrices. Here we present PoPS, a publicly accessible bioinformatics tool () that provides a novel method for building computational models of protease specificity, which while still being based on these amino acid sequences, can be built from any experimental data or expert knowledge available to the user. PoPS specificity models can be used to predict and rank likely cleavages within a single substrate, and within entire proteomes. Other factors, such as the secondary or tertiary structure of the substrate, can be used to screen unlikely sites. Furthermore, the tool also provides facilities to infer, compare and test models, and to store them in a publicly accessible database.

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