scholarly journals Primary Sequence and 3D Structure Prediction of the Plant Toxin Stenodactylin

Toxins ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 538
Author(s):  
Rosario Iglesias ◽  
Letizia Polito ◽  
Massimo Bortolotti ◽  
Manuela Pedrazzi ◽  
Lucía Citores ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structure Prediction ◽  
3D Structure ◽  
Nucleotide Sequence Analysis ◽  
Primary Sequence ◽  
3D Structure Prediction ◽  
A Chain

Stenodactylin is one of the most potent type 2 ribosome-inactivating proteins (RIPs); its high toxicity has been demonstrated in several models both in vitro and in vivo. Due to its peculiarities, stenodactylin could have several medical and biotechnological applications in neuroscience and cancer treatment. In this work, we report the complete amino acid sequence of stenodactylin and 3D structure prediction. The comparison between the primary sequence of stenodactylin and other RIPs allowed us to identify homologies/differences and the amino acids involved in RIP toxic activity. Stenodactylin RNA was isolated from plant caudex, reverse transcribed through PCR and the cDNA was amplificated and cloned into a plasmid vector and further analyzed by sequencing. Nucleotide sequence analysis showed that stenodactylin A and B chains contain 251 and 258 amino acids, respectively. The key amino acids of the active site described for ricin and most other RIPs are also conserved in the stenodactylin A chain. Stenodactylin amino acid sequence shows a high identity degree with volkensin (81.7% for A chain, 90.3% for B chain), whilst when compared with other type 2 RIPs the identity degree ranges from 27.7 to 33.0% for the A chain and from 42.1 to 47.7% for the B chain.

scholarly journals Sequence, Structure, and Binding Site Analysis of Kirkiin in Comparison with Ricin and Other Type 2 RIPs

Toxins ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 862
Author(s):  
Stefania Maiello ◽  
Rosario Iglesias ◽  
Letizia Polito ◽  
Lucía Citores ◽  
Massimo Bortolotti ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Structure Prediction ◽  
3D Structure ◽  
Binding Activity ◽  
Amino Acid Residues ◽  
Reading Frame ◽  
A Chain

Kirkiin is a new type 2 ribosome-inactivating protein (RIP) purified from the caudex of Adenia kirkii with a cytotoxicity compared to that of stenodactylin. The high toxicity of RIPs from Adenia genus plants makes them interesting tools for biotechnology and therapeutic applications, particularly in cancer therapy. The complete amino acid sequence and 3D structure prediction of kirkiin are here reported. Gene sequence analysis revealed that kirkiin is encoded by a 1572 bp open reading frame, corresponding to 524 amino acid residues, without introns. The amino acid sequence analysis showed a high degree of identity with other Adenia RIPs. The 3D structure of kirkiin preserves the overall folding of type 2 RIPs. The key amino acids of the active site, described for ricin and other RIPs, are also conserved in the kirkiin A chain. Sugar affinity studies and docking experiments revealed that both the 1α and 2γ sites of the kirkiin B chain exhibit binding activity toward lactose and D-galactose, being lower than ricin. The replacement of His246 in the kirkiin 2γ site instead of Tyr248 in ricin causes a different structure arrangement that could explain the lower sugar affinity of kirkiin with respect to ricin.

scholarly journals Protein structure prediction

2018 ◽  
Vol 32 (18) ◽  
pp. 1840009 ◽  
Author(s):  
Haiyou Deng ◽  
Ya Jia ◽  
Yang Zhang
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Computational Biology ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
3D Structure ◽  
Critical Assessment ◽  
Prediction Methods ◽  
Recent Effort

Predicting 3D structure of protein from its amino acid sequence is one of the most important unsolved problems in biophysics and computational biology. This paper attempts to give a comprehensive introduction of the most recent effort and progress on protein structure prediction. Following the general flowchart of structure prediction, related concepts and methods are presented and discussed. Moreover, brief introductions are made to several widely-used prediction methods and the community-wide critical assessment of protein structure prediction (CASP) experiments.

PROTEIN TERTIARY STRUCTURE PREDICTION BASED ON MAIN CHAIN ANGLE USING A HYBRID BEES COLONY OPTIMIZATION ALGORITHM

2012 ◽  
Vol 09 ◽  
pp. 143-156 ◽  
Author(s):  
ZAKARIA N. MAHMOOD ◽  
MASSUDI MAHMUDDIN ◽  
MOHAMMED NOORALDEEN MAHMOOD
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Optimization Algorithm ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Promising Result ◽  
3D Structure ◽  
Research Area ◽  
Prototype System ◽  
Protein Tertiary Structure

Encoding proteins of amino acid sequence to predict classified into their respective families and subfamilies is important research area. However for a given protein, knowing the exact action whether hormonal, enzymatic, transmembranal or nuclear receptors does not depend solely on amino acid sequence but on the way the amino acid thread folds as well. This study provides a prototype system that able to predict a protein tertiary structure. Several methods are used to develop and evaluate the system to produce better accuracy in protein 3D structure prediction. The Bees Optimization algorithm which inspired from the honey bees food foraging method, is used in the searching phase. In this study, the experiment is conducted on short sequence proteins that have been used by the previous researches using well-known tools. The proposed approach shows a promising result.

Complete Covalent Structure of Human Platelet Factor 4

1979 ◽  
Vol 42 (05) ◽  
pp. 1652-1660 ◽  
Author(s):  
Francis J Morgan ◽  
Geoffrey S Begg ◽  
Colin N Chesterman
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Human Platelet ◽  
Platelet Factor 4 ◽  
Platelet Factor ◽  
Disulphide Bonds ◽  
Covalent Structure

SummaryThe amino acid sequence of the subunit of human platelet factor 4 has been determined. Human platelet factor 4 consists of identical subunits containing 70 amino acids, each with a molecular weight of 7,756. The molecule contains no methionine, phenylalanine or tryptophan. The proposed amino acid sequence of PF4 is: Glu-Ala-Glu-Glu-Asp-Gly-Asp-Leu-Gln-Cys-Leu-Cys-Val-Lys-Thr-Thr-Ser- Gln-Val-Arg-Pro-Arg-His-Ile-Thr-Ser-Leu-Glu-Val-Ile-Lys-Ala-Gly-Pro-His-Cys-Pro-Thr-Ala-Gin- Leu-Ile-Ala-Thr-Leu-Lys-Asn-Gly-Arg-Lys-Ile-Cys-Leu-Asp-Leu-Gln-Ala-Pro-Leu-Tyr-Lys-Lys- Ile-Ile-Lys-Lys-Leu-Leu-Glu-Ser. From consideration of the homology with p-thromboglobulin, disulphide bonds between residues 10 and 36 and between residues 12 and 52 can be inferred.

scholarly journals Effect of co-ingestion of amino acids with rice on glycaemic and insulinaemic response

2015 ◽  
Vol 114 (11) ◽  
pp. 1845-1851 ◽  
Author(s):  
Yean Yean Soong ◽  
Joseph Lim ◽  
Lijuan Sun ◽  
Christiani Jeyakumar Henry
Keyword(s):  
Amino Acids ◽  
Blood Glucose ◽  
Amino Acid ◽  
Glycaemic Index ◽  
Amino Acid Mixture ◽  
Postprandial Blood Glucose ◽  
Acid Mixture ◽  
White Rice ◽  
Amino Acid Mixtures

AbstractConsumption of high glycaemic index (GI) and glycaemic response (GR) food such as white rice has been implicated in the development of type 2 diabetes. Previous studies have reported the ability of individual amino acids to reduce GR of carbohydrate-rich foods. Because of the bitter flavour of amino acids, they have rarely been used to reduce GR. We now report the use of a palatable, preformed amino acid mixture in the form of essence of chicken. In all, sixteen healthy male Chinese were served 68 or 136 ml amino acid mixture together with rice, or 15 or 30 min before consumption of white rice. Postprandial blood glucose and plasma insulin concentrations were measured at fasting and every 15 min after consumption of the meal until 60 min after the consumption of the white rice. Subsequent blood samples were taken at 30-min intervals until 210 min. The co-ingestion of 68 ml of amino acid mixture with white rice produced the best results in reducing the peak blood glucose and GR of white rice without increasing the insulinaemic response. It is postulated that amino acid mixtures prime β-cell insulin secretion and peripheral tissue uptake of glucose. The use of ready-to-drink amino acid mixtures may be a useful strategy for lowering the high-GI rice diets consumed in Asia.

SOME ASPECTS OF THE STRUCTURE OF HEMOGLOBIN

1964 ◽  
Vol 42 (6) ◽  
pp. 755-762 ◽  
Author(s):  
David B. Smith
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Partial Amino Acid Sequence ◽  
Heme Pocket ◽  
Terminal Amino ◽  
Polypeptide Chains ◽  
Kinetics Of ◽  
Β Chain

An outline of present ideas concerning the arrangement, folding, and chemistry of the polypeptide chains of hemoglobin is given with some references to present know ledge of myoglobin.New material includes a partial amino acid sequence of the β-chain of horse hemoglobin, details concerning the amino acids lining the heme pocket of horse hemoglobin, and the effects of carboxypeptidases A and B on horse oxy- and horse deoxy-hemoglobin. The kinetics of the latter reactions are not simple. The C-terminal amino acids are released more rapidly from the oxygenated form.

scholarly journals The amino acid sequence of cytochromes c-551 from three species of Pseudomonas

1973 ◽  
Vol 131 (3) ◽  
pp. 485-498 ◽  
Author(s):  
R. P. Ambler ◽  
Margaret Wynn
Keyword(s):  
Amino Acids ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Cytochrome C ◽  
Amino Acid Sequence ◽  
Amino Acid Sequences ◽  
Mitochondrial Cytochrome ◽  
Cytochromes C ◽  
Lending Library ◽  
Single Peptide

The amino acid sequences of the cytochromes c-551 from three species of Pseudomonas have been determined. Each resembles the protein from Pseudomonas strain P6009 (now known to be Pseudomonas aeruginosa, not Pseudomonas fluorescens) in containing 82 amino acids in a single peptide chain, with a haem group covalently attached to cysteine residues 12 and 15. In all four sequences 43 residues are identical. Although by bacteriological criteria the organisms are closely related, the differences between pairs of sequences range from 22% to 39%. These values should be compared with the differences in the sequence of mitochondrial cytochrome c between mammals and amphibians (about 18%) or between mammals and insects (about 33%). Detailed evidence for the amino acid sequences of the proteins has been deposited as Supplementary Publication SUP 50015 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973), 131, 5.

scholarly journals Amino acid sequence of the human fibronectin receptor.

1987 ◽  
Vol 105 (3) ◽  
pp. 1183-1190 ◽  
Author(s):  
W S Argraves ◽  
S Suzuki ◽  
H Arai ◽  
K Thompson ◽  
M D Pierschbacher ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Calcium Binding ◽  
Beta Subunit ◽  
Alpha Subunit ◽  
Receptor Subunit ◽  
Fibronectin Receptor ◽  
Adhesion Receptor ◽  
Receptor Beta

The amino acid sequence deduced from cDNA of the human placental fibronectin receptor is reported. The receptor is composed of two subunits: an alpha subunit of 1,008 amino acids which is processed into two polypeptides disulfide bonded to one another, and a beta subunit of 778 amino acids. Each subunit has near its COOH terminus a hydrophobic segment. This and other sequence features suggest a structure for the receptor in which the hydrophobic segments serve as transmembrane domains anchoring each subunit to the membrane and dividing each into a large ectodomain and a short cytoplasmic domain. The alpha subunit ectodomain has five sequence elements homologous to consensus Ca2+-binding sites of several calcium-binding proteins, and the beta subunit contains a fourfold repeat strikingly rich in cysteine. The alpha subunit sequence is 46% homologous to the alpha subunit of the vitronectin receptor. The beta subunit is 44% homologous to the human platelet adhesion receptor subunit IIIa and 47% homologous to a leukocyte adhesion receptor beta subunit. The high degree of homology (85%) of the beta subunit with one of the polypeptides of a chicken adhesion receptor complex referred to as integrin complex strongly suggests that the latter polypeptide is the chicken homologue of the fibronectin receptor beta subunit. These receptor subunit homologies define a superfamily of adhesion receptors. The availability of the entire protein sequence for the fibronectin receptor will facilitate studies on the functions of these receptors.

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