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Search Results: 1 - 10 of 1284 matches for " Disulfide bond "
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A Prediction Method of Protein Disulfide Bond Based on Hybrid Strategy  [PDF]
Pengfei Sun, Yunhong Ding, Yuyan Huang, Lei Zhang
Journal of Biomedical Science and Engineering (JBiSE) , 2016, DOI: 10.4236/jbise.2016.910B015
A prediction method of protein disulfide bond based on support vector machine and sample selection is proposed in this paper. First, the protein sequences selected are en-coded according to a certain encoding, input data for the prediction model of protein disulfide bond is generated; Then sample selection technique is used to select a portion of input data as training samples of support vector machine; finally the prediction model training samples trained is used to predict protein disulfide bond. The result of simulation experiment shows that the prediction model based on support vector ma-chine and sample selection can increase the prediction accuracy of protein disulfide bond.
Prediction Method of Protein Disulfide Bond Based on Pattern Selection  [PDF]
Pengfei Sun, Yuanquan Cui, Tiankai Chen, Ying Zhao
Engineering (ENG) , 2013, DOI: 10.4236/eng.2013.510B083

The effect of the different training samples is different for the classifier when pattern recognition system is established. The training samples were selected randomly in the past protein disulfide bond prediction methods, therefore the prediction accuracy of protein contact was reduced. In order to improve the influence of training samples, a prediction method of protein disulfide bond on the basis of pattern selection and Radical Basis Function neural network has been brought forward in this paper. The attributes related with protein disulfide bond are extracted and coded in the method and pattern selection is used to select training samples from coded samples in order to improve the precision of protein disulfide bond prediction. 200 proteins with disulfide bond structure from the PDB database are encoded according to the encoding approach and are taken as models of training samples. Then samples are taken on the pattern selection based on the nearest neighbor algorithm and corresponding prediction models are set by using RBF neural network. The simulation experiment result indicates that this method of pattern selection can improve the prediction accuracy of protein disulfide bond.

Amino Acid Patterns around Disulfide Bonds
José R. F. Marques,Rute R. da Fonseca,Brett Drury,André Melo
International Journal of Molecular Sciences , 2010, DOI: 10.3390/ijms11114673
Abstract: Disulfide bonds provide an inexhaustible source of information on molecular evolution and biological specificity. In this work, we described the amino acid composition around disulfide bonds in a set of disulfide-rich proteins using appropriate descriptors, based on ANOVA (for all twenty natural amino acids or classes of amino acids clustered according to their chemical similarities) and Scheffé (for the disulfide-rich proteins superfamilies) statistics. We found that weakly hydrophilic and aromatic amino acids are quite abundant in the regions around disulfide bonds, contrary to aliphatic and hydrophobic amino acids. The density distributions (as a function of the distance to the center of the disulfide bonds) for all defined entities presented an overall unimodal behavior: the densities are null at short distances, have maxima at intermediate distances and decrease for long distances. In the end, the amino acid environment around the disulfide bonds was found to be different for different superfamilies, allowing the clustering of proteins in a biologically relevant way, suggesting that this type of chemical information might be used as a tool to assess the relationship between very divergent sets of disulfide-rich proteins.
Function of disulflde bond Cys45-Cys50 of prochymosin
TANG Bing,YANG Kaiyu,

中国科学C辑(英文版) , 1996,
Abstract: The conditions (temperature, time, pH) for solubilizing inclusion bodies of prochymosin mutant, Cys45Asp/Cys50Ser, are identical with those for the wild type. Moreover, they have similar oxidative refolding behavior. Under the same renaturation conditions both of them can undergo correct refolding leading to the formation of activable molecules. This is quite different from the mutant with deletion of Cys250-Cys283, indicating that Cys45-Cys50 contributes less to the correct refolding of prochymosin than Cys250- Cys283. However, deletion of Cys45-Cys50 results in a remarkable decrease of the thermostability of pseudochymosin, suggesting that this disulfide bond plays an important role in stabilizing enzyme conformation. The proteolytic (P) and milk-dotting (C) activities of the mutant of pseudochymosin, Cys45Asp/Cys50Ser, are lower than those of its wild counterpart. The C/P ratio of the former is onefold higher than that of the latter.
Structural and dynamic effects of changing the pattern of disulfide bonds in the vascular endothelial growth factor [Efeito estrutural e dinamico da altera o do padr o de liga es dissulfeto do fator de crescimento vascular endotelial]
Bruno A. C. Horta,Ricardo B. de Alencastro
Revista Virtual de Química , 2011,
Abstract: The vascular endothelial growth factor (VEGF) is a key mediator of angiogenesis and is related toseveral physiological and pathological processes. VEGF is a dimeric protein that belongs to a superfamily ofproteins that include in their structures a set of disulfide bonds forming the so called cystine knot. The presenceof these disulfide bonds in the structure of VEGF is related to its biological activity, but is not responsible to itsthermodynamic stability. The present study aims at the investigation via molecular dynamics simulations of theeffects of mutations of cysteine residues on the structure and dynamics of VEGF. Modified models (i.e. mutants)of VEGF are constructed by replacing certain cysteine residues by alanine or serine residues in such a way thatselected dissulfide bonds are broken. Molecular dynamics simulations of these models are then carried out andthe results are compared to the ones previously obtained for the native structure (WT: wild type) and to therespective crystalographic structures of the mutants. The simulations indicate that the replacement of cysteineresidues by alanine or serine promote localized structural changes, basically affecting the loop-2, which islocalized at the receptor-binding region.
Inter-protein bonding and other molecular interactions in hen egg white
Journal of the Serbian Chemical Society , 2000,
Abstract: The analysis of the SDS-polyacrylamide gel electrophoresis (SDS-PAGE) data, combined with the comparison of viscosity data corresponding to the thin fraction of hen egg white and 2 mM purefied ovalbumin solution, showed that the thin fraction is a protein solution. Dissolution of the thick fraction of hen egg white in SDS and urea solutions followed by SDS-PAGE, in the presence or absence of b-mercaptoethanol, revealed that it is a protein gel. It was also found that the gel structure consists of the three-dimensional ovomucine-ovomucoid network (matrix) held together by S-S bridges which captures the rest of the proteins (ovalbumin, conalbumin, etc). The captured proteins can also be interconnected by S-S bridges thus forming agglomerates or conglomerates, but they are predominantly held by weak electrostatic interactions, as demonstrated by the washing out and dissolving experiments. The matrix structure does not prevent denaturation of the captured proteins as indecated by the 50% decrease in turbidity following gel swelling by the addition of 1 part of an 8 M urea solution to 9 parts of the gel.
Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis
Yoshiaki Furukawa
Frontiers in Cellular Neuroscience , 2013, DOI: 10.3389/fncel.2013.00240
Abstract: Dominant mutations in Cu,Zn-superoxide dismutase (SOD1) cause a familial form of amyotrophic lateral sclerosis (fALS). Misfolding and aggregation of mutant SOD1 proteins are a pathological hallmark of SOD1-related fALS cases; however, the molecular mechanism of SOD1 aggregation remains controversial. Here, I have used E. coli as a model organism and shown multiple distinct pathways of SOD1 aggregation that are dependent upon its thiol-disulfide status. Overexpression of fALS-mutant SOD1s in the cytoplasm of E. coli BL21 and SHuffleTM, where redox environment is reducing and oxidizing, respectively, resulted in the formation of insoluble aggregates with notable differences; a disulfide bond of SOD1 was completely reduced in BL21 or abnormally formed between SOD1 molecules in SHuffleTM. Depending upon intracellular redox environment, therefore, mutant SOD1 is considered to misfold/aggregate through distinct pathways, which would be relevant in description of the pathological heterogeneity of SOD1-related fALS cases.
Synthesis, Characterization and Crystal Structure of a New Schiff Base Ligand from a Bis(Thiazoline) Template and Hydrolytic Cleavage of the Imine Bond Induced by a Co(II) Cation  [PDF]
Jafar Attar Gharamaleki, Fahimeh Akbari, Akram Karbalaei, Kamran B. Ghiassi, Marilyn M. Olmstead
Open Journal of Inorganic Chemistry (OJIC) , 2016, DOI: 10.4236/ojic.2016.61005
Abstract: The reaction of bis-[2-amino-4-pheny1-5-thiazolyl] disulfide with 5-nitro-salicylaldehyde in absolute ethanol resulted in the formation of a new Schiff base ligand H2L (1). Characterization of the ligand was performed by FT-IR, 1H NMR, 13C NMR, UV-Vis, elemental analysis and single crystal X-ray diffraction. The ligand, (1), possesses a disulfide –S–S– bridge of 2.1121 (3) ? length, and the molecule adopts a cis-conformation around this bond. In the crystal structure of (1), an intramolecular O–H···N hydrogen bond with D… A distance of 2.69 (3) ? was present. The reaction of (1) with Co(NO3)2·6H2O and CuCl2·2H2O in methanol afforded the corresponding metal complexes. The obtained solids were further investigated by elemental analysis and UV-Vis titration that confirmed the formation of [CoL] and [ClCuHL] complexes. However, recrystallizaion of the Co(II) complex in dimethylsulfoxide caused the complete hydrolysis of the imine bond and afforded a Co(II) complex in which two 5-nitro-salicylaldehyde and two DMSO molecules were coordinated to the central metal in an octahedral fashion. This structure (2) was also confirmed by single crystal X-ray analysis.
SHuffle, a novel Escherichia coli protein expression strain capable of correctly folding disulfide bonded proteins in its cytoplasm
Julie Lobstein, Charlie A Emrich, Chris Jeans, Melinda Faulkner, Paul Riggs, Mehmet Berkmen
Microbial Cell Factories , 2012, DOI: 10.1186/1475-2859-11-56
Abstract: We have engineered a new E. coli protein expression strain named SHuffle, dedicated to producing correctly disulfide bonded active proteins to high yields within its cytoplasm. This strain is based on the trxB gor suppressor strain SMG96 where its cytoplasmic reductive pathways have been diminished, allowing for the formation of disulfide bonds in the cytoplasm. We have further engineered a major improvement by integrating into its chromosome a signal sequenceless disulfide bond isomerase, DsbC. We probed the redox state of DsbC in the oxidizing cytoplasm and evaluated its role in assisting the formation of correctly folded multi-disulfide bonded proteins. We optimized protein expression conditions, varying temperature, induction conditions, strain background and the co-expression of various helper proteins. We found that temperature has the biggest impact on improving yields and that the E. coli B strain background of this strain was superior to the K12 version. We also discovered that auto-expression of substrate target proteins using this strain resulted in higher yields of active pure protein. Finally, we found that co-expression of mutant thioredoxins and PDI homologs improved yields of various substrate proteins.This work is the first extensive characterization of the trxB gor suppressor strain. The results presented should help researchers design the appropriate protein expression conditions using SHuffle strains.
Stabilization of the Single-Chain Fragment Variable by an Interdomain Disulfide Bond and Its Effect on Antibody Affinity
Jian-Xin Zhao,Lian Yang,Zhen-Nan Gu,Hai-Qin Chen,Feng-Wei Tian,Yong-Quan Chen,Hao Zhang,Wei Chen
International Journal of Molecular Sciences , 2011, DOI: 10.3390/ijms12010001
Abstract: The interdomain instability of single-chain fragment variable (scFv) might result in intermolecular aggregation and loss of function. In the present study, we stabilized H4—an anti-aflatoxin B 1 (AFB 1) scFv—with an interdomain disulfide bond and studied the effect of the disulfide bond on antibody affinity. With homology modeling and molecular docking, we designed a scFv containing an interdomain disulfide bond between the residues H44 and L100. The stability of scFv (H4) increased from a GdnHCl 50 of 2.4 M to 4.2 M after addition of the H44-L100 disulfide bond. Size exclusion chromatography revealed that the scFv (H44-L100) mutant existed primarily as a monomer, and no aggregates were detected. An affinity assay indicated that scFv (H4) and the scFv (H44-L100) mutant had similar IC 50 values and affinity to AFB 1. Our results indicate that interdomain disulfide bonds could stabilize scFv without affecting affinity.
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