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ABSTRACT: Kappa-Hefutoxin1 is a K(+) channel-blocking toxin from the scorpion Heterometrus fluvipes. It is a 22-residue protein that adapts a novel fold of two parallel helices linked by two disulfide bridges without beta-sheets. Recognition of interactions of kappa-Hefutoxin1 with the voltage-gated potassium channels, Kv1.1, Kv1.2, and Kv1.3, was studied by 3D-Dock software package. All structures of kappa-Hefutoxin1 were considered during the simulations, which indicated that even small changes in the structure of kappa-Hefutoxin1 considerably affected both the recognition and the binding between kappa-Hefutoxin1 and the Kv1 channels. kappa-Hefutoxin1 is located around the extracellular part of the Kv1 channels, making contacts with its helices. Lys 19, Tyr 5, Arg 6, Trp 9, or Arg 10 in the toxin and residues Asp 402, His 404, Thr 407,Gly 401, and Asp 386 in each subunit of the Kv potassium channel are the key residues for the toxin-channel recognition. Moreover, the simulation result demonstrates that the hydrophobic interactions are important in interaction of negatively charged toxins with potassium channels. The results of our docking/molecular dynamics simulations indicate that our 3D model structure of the kappa-Hefutoxin1-complex is both reasonable and acceptable and could be helpful for smarter drug design and the blocking agents of Kv1 channels.
Proteins Structure Function and Bioinformatics 06/2008; 71(3):1441-9. · 3.39 Impact Factor
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BMC Systems Biology. 01/2007;
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ABSTRACT: Thermostability of proteins in general and especially thermophilic proteins has been subject of a wide variety of studies based on theoretical and experimental investigation. Thermostability seems to be a property obtained through many minor structural modifications rather than certain amino acids substitution. In comparison with its mesophile homologue in a thermostable protein, usually a number of amino acids are exchanged. A wide variety of theoretical studies are based on comparative investigation of thermophilic proteins characteristics with their mesophilic counterparts in order to reveal their sequences, structural differences and consequently, to relate these observed differences to the thermostability properties. In this work we have compared a dataset of thermophilic proteins with their mesophilic homologues and furthermore, a mesophilic proteins dataset was also compared with its mesophilic homologue. This strategy enabled us first, to eliminate noise or background differences from signals and moreover, the important factors which were related to the thermostability were recognized too. Our results reveal that thermophilic and mesophilic proteins have both similar polar and nonpolar contribution to the surface area and compactness. On the other hand, salt bridges and main chain hydrogen bonds show an increase in the majority of thermophilic proteins in comparison to their mesophilic homologues. In addition, in thermophilic proteins hydrophobic residues are significantly more frequent, while polar residues are less. These findings indicate that thermostable proteins through evolution adopt several different strategies to withstand high temperature environments.
Biophysical Chemistry 03/2006; 119(3):256-70. · 2.20 Impact Factor
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ABSTRACT: Amphibians have a large variety of antimicrobial peptides that serve as natural innate barriers limiting microbial infection or, in some instances, act as an integral component in response to inflammation or microbial infection. A novel peptide with antibacterial effects and without hemolytic activity was purified from skin secretions of Rana ridibunda by multisteps cation-exchange FPLC, reversed-phase HPLC and was called Ridibundin 1. Circular dichroism spectra revealed that this peptide strongly prefers to form an amphipathic α-helical structure in the presence of 50% trifluoroethanol. Acting as wide-spectrum microbicides against a variety of bacteria, Ridibundin 1 also shows no hemolytic activity on erythrocyte. These properties reveal its unique characteristics and potential therapeutic application.
Islamic Republic of Iran. 01/2004; 15:303-309.
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ABSTRACT: A comparative study was performed on the effect of calcium on native and chemically modified forms of mesophilic and thermophilic alpha-amylases. Circular dichroism (CD) and irreversible thermoinactivation studies were carried out in the absence and presence of 10 mM calcium. From the CD experiments, changes in the tertiary structure of these enzymes, brought about by modification, were concluded. Furthermore, these changes were found to be influenced by the presence of calcium. Sorbitol was very effective in affording protection against irreversible thermoinactivation of native and modified forms of the enzymes, both in the absence and presence of calcium. Results are discussed in terms of the usefulness of this new approach involving a combination of medium and chemical modification for protein stabilization and enhancement of catalytic potential.
Biochimica et Biophysica Acta 09/2001; 1548(2):229-37. · 4.66 Impact Factor
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ABSTRACT: Chemical modification of lysine residues in two bacterial alpha-amylases, a mesophilic enzyme from Bacillus amyloliquefaciens (BAA) and a thermophilic enzyme from Bacillus licheniformis (BLA) was carried out using citraconic anhydride. 13 +/- 1 residues in BAA and 10 +/- 1 residues in BLA were found modified under defined experimental conditions. Modification brought about dramatic enhancement of thermal stability of BAA and catalytic activity of BLA. Such alterations were found dependent on the temperature and pH. Results obtained on Tm, the extent of deamidation, changes in the circular dichroism (CD) spectra and kinetic parameters before and after modification are discussed in terms of their contributions to the mechanism of irreversible thermoinactivation and activity enhancement.
Enzyme and microbial technology. 05/2001; 28(6):543-549.
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ABSTRACT: A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair-information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60 %, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case.
Proteins Structure Function and Bioinformatics 04/2001; 42(4):452-9. · 3.39 Impact Factor
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ABSTRACT: The 3-D structural information is a prerequisite for a rational ligand design. In the absence of experimental data, model building on the basis of a known 3-D structure of a homologous protein is at present the only reliable method to obtain structural information. A homology model building study of the pyridoxal 5'-phosphate (PLP)-dependent histidine decarboxylase from Morganella morganii (HDC-MM) has been carried out based on the crystal structure of the aspartate aminotransferase from Escherichia coli (AAT-EC). The primary sequences of AAT-EC and HDC-MM were aligned by automated alignment procedure. A 3-D model of HDC-MM was constructed by copying the coordinates of the residues from the crystal structure of AAT-EC into the corresponding residues in HDC-MM. After energy-minimization of the resulting 3-D model of HDC-MM, possible active site residues were identified by fitting the substrate (l-histidine) into the proposed active-site. In our model, several residues, which have an important role in the AAT-EC active-site, are located in positions spatially identical to those in AAT-EC structure. The back-bone of the modelled active site pocket is constructed by residues; Gly-92, Gly-93, Thr-93, Ser-115, Asp-200, Ala-202, Ser-229 and Lys-232 together with residues Asn-8, His-119, Thr-171, His-198, Leu-203, His-231, Ser-236 and Ile-238. In the ligand binding site, it appears that the HDC-MM model will position l-histidine (substrate) in the area consisting of the residues; Glu-29, Ser-30, Leu-38, His-231 and Lys-232. The nitrogen atom of the imidazole ring (N2) of the substrate is predicted to interact with the carboxylate group of Ser-30. The alpha-carboxylate of histidine points toward the Lys-232 to have electrostatic interaction with its side chain nitrogen atom (N(Z)). In conclusion, this combination of sequence and 3-D structural homology between AAT-EC and HDC-MM model could provide insight in assigning the probable active site residues.
European Journal of Medicinal Chemistry 07/2000; 35(6):567-76. · 3.35 Impact Factor
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ABSTRACT: Histidine decarboxylase catalyses the decarboxylation of l-histidine to histamine using pyridoxal-5'-phosphate (PLP) as coenzyme. The PM3 quantum mechanical conformation method of analysis and heat of formation calculation were carried out for intermediates which are probably formed during the interaction of histidine (substrate), (s)-alpha-methylhistidine, (s)-alpha-hydrazinohistidine, (s)-alpha-fluoromethylhistidine and (s)-alpha-difluoromethylhistidine (inhibitors) with PLP-dependent histidine decarboxylase from Morganella morganii. The results suggest that the structures of the intermediates before and after decarboxylation were found to exist in a conformation showing a planar arrangement of the double bonds with the pyridoxylidene ring and the bond to the carboxyl group being perpendicular to this plane. After decarboxylation, all the double bonds are in the plane of the pyridoxylidene ring which facilitates the electron displacement for the following protonation at C(alpha). The values of the enthalpy for intermediates would increase the probability of their formation in the enzyme's active site which are consistent with all available stereochemical and mechanistic data.
European Journal of Medicinal Chemistry 04/2000; 35(3):283-9. · 3.35 Impact Factor
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ABSTRACT: The present communication reports on changes in the secondary and tertiary structures of native and apo-yeast alcohol dehydrogenase upon heating at 50 °C, as evident from circular dichroism (CD) studies. The presence of sugars provided significant protection with trehalose being the most effective. Exposure of hydrophobic clusters in the protein molecule upon heat denaturation was confirmed by fluorescence studies using 1-anilinonaphthalene-8-sulfonate (ANS) as a hydrophobic reporter probe. All sugars, and especially trehalose, reduced the affinity of both forms of the enzyme for this probe. The effectiveness of sugars in diminishing ANS fluorescence enhancement is in accordance with their ability to protect aggregation of the proteins, reported earlier [Miroliaei M, Nemat-Gorgani M. Sugars protect native and apo yeast alcohol dehydrogenase against irreversible thermoinactivation. Enzyme Microb Technol 2001;29:554–9]. It is concluded that prevention of the mechanisms of irreversible thermoinactivation may occur with retention of the secondary and tertiary structural properties of the proteins.
Enzyme and Microbial Technology.
