Distribution Of Secondary Structural Elements Research Articles

Protein Structural Class Prediction Based on Distance-related Statistical Features from Graphical Representation of Predicted Secondary Structure

Protein structural class prediction is beneficial to protein structure and function analysis. Exploring good feature representation is a key step for this prediction task. Prior works have demonstrated the effectiveness of the secondary structure based feature extraction methods especially for lowsimilarity protein sequences. However, the prediction accuracies still remain limited. To explore the potential of secondary structure information, a novel feature extraction method based on a generalized chaos game representation of predicted secondary structure is proposed. Each protein sequence is converted into a 20-dimensional distance-related statistical feature vector to characterize the distribution of secondary structure elements and segments. The feature vectors are then fed into a support vector machine classifier to predict the protein structural class. Our experiments on three widely used lowsimilarity benchmark datasets (25PDB, 1189 and 640) show that the proposed method achieves superior performance to the state-of-the-art methods. It is anticipated that our method could be extended to other graphical representations of protein sequence and be helpful in future protein research.

Structural Analysis of CD59 of Chinese Tree Shrew: A New Reference Molecule for Human Immune System Specific CD59 Drug Discovery.

Chinese tree shrews (Tupaia belangeri chinensis) bear several characteristics that are considered to be very crucial for utilizing in animal experimental models in biomedical research. Subsequent to the identification of key aspects and signaling pathways in nervous and immune systems, it is revealed that tree shrews acquire common as well as unique characteristics, and hence offer a genetic basis for employing them as a prospective model for biomedical research. CD59 glycoprotein, commonly referred to as MAC-inhibitory protein (MAC-IP), membrane inhibitor of reactive lysis (MIRL), or protectin, is encoded by the CD59 gene in human beings. It is the member of the LY6/uPAR/alpha-neurotoxin protein family. With this initial point, the objective of this study was to determine a comparative composite based structure of CD59 of Chinese tree shrew. The additional objective of this study was to examine the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the assistance of several bioinformatical analytical tools. CD59 Amino acid sequence of Chinese tree shrew was collected from the online database system of National Centre for Biotechnology Information. SignalP 4.0 online server was employed for detection of signal peptide instance within the protein sequence of CD59. Molecular model structure of CD59 protein was generated by the Iterative Threading ASSEmbly Refinement (I-TASSER) suite. The confirmation for three-dimensional structural model was evaluated by structure validation tools. Location of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of Chimera tool. Electrostatic potential analysis was carried out with the adaptive Poisson-Boltzmann solver package. Subsequently validated model was used for the functionally critical amino acids and active site prediction. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program. Analysis of Ramachandran plot for Chinese tree shrew depicted that overall, 100% of the residues in homology model were observed in allowed and favored regions, sequentially leading to the validation of the standard of generated protein structural model. In case of CD59 of Chinese tree shrew, the total score of G-factor was found to be -0.66 that was generally larger than the acceptable value. This approach suggests the significance and acceptability of the modeled structure of CD59 of Chinese tree shrew. The molecular model data in cooperation to other relevant post model analysis data put forward molecular insight into protecting activity of CD59 protein molecule of Chinese tree shrew. In the present study, we have proposed the first molecular model structure of uncharted CD59 of Chinese tree shrew by significantly utilizing the comparative composite modeling approach. Therefore, the development of a structural model of the CD59 protein was carried out and analyzed further for deducing molecular enrichment technique. The collaborative effort of molecular model and other relevant data of post model analysis carry forward molecular understanding to protecting activity of CD59 functions towards better insight of features of this natural lead compound.

THE BIOPHYSICAL CHARACTERISTICS AND STRUCTURAL EXPLORATION OF PROGRAMMED CELL DEATH REGULATOR B-CELL LYMPHOMA 2-ASSOCIATED X PROTEIN OF CHINESE LIVER FLUKE (CLONORCHIS SINENSIS)

Objective: The balance between deaths and cellular life is regulated by B-cell lymphoma 2 (BCL-2)-associated X protein (BAX) an important pro-apoptotic components of BCL-2 family. With this initial point, the aim of this study was to determine a comparative composite based structure of BAX of Chinese liver fluke and different structural analysis.Methods: Protein amino acid of BAX of Chinese liver fluke mined from National Centre for Biotechnology Information (http://ncbi.nlm.nih.gov). Molecular model of BAX of Chinese liver fluke protein was generated by the comparative composite modeling tool Iterative Threading ASSEmbly Refinement suite. Afterward, I-TASSER generated molecular model was subjected to further structural improvements by energy minimization step. Distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, and hydrophobicity molecular surface analysis was performed with the help of bioinformatical tools.Results: Analysis of Ramachandran plot created by PROCHECK tool is a consensus standard for validation purpose of protein structural modeling. Altogether 97.8% of the residues were detected in allowed and favored regions, which in turn validate the quality of generated protein structural model. Total negatively and positively charged residues within the BAX of Chinese liver fluke were 23 and 20, respectively. Chimera package-guided hydrophobicity molecular surface analysis illustrates that molecule specific hydrophobicity surface is exclusive to BAX protein molecule.Conclusion: Within the scope of this scientific investigation, we have successfully utilized molecular modeling approach to suggest the first molecular three-dimensional model structure of BAX of Chinese liver fluke. The synchronous balance between cellular deaths and cellular life is keeping up by BAX, an important pro-apoptotic family member of BCL-2 family. Consequently, it would be an exciting approach to resolve its structural characterization and molecular structure to propose mode of mechanism action.

Discovery of an Unexplored Protein Structural Scaffold of Serine Protease from Big Blue Octopus (Octopus cyanea): A New Prospective Lead Molecule.

Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system. Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique. Our key aim was to propose the first molecular model structure of unexplored serine protease 5 derived from big blue octopus. The other objective of this study was to analyze the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the aid of different bioinformatic tools. In the present study, molecular model has been generated with the help of I-TASSER suite. Afterwards the refined structural model was validated with standard methods. For functional annotation of protein molecule we used Protein Information Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with different bioinformatical algorithms for the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program. The molecular model data in cooperation to other pertinent post model analysis data put forward molecular insight to proteolytic activity of serine protease 5, which helps in the clear understanding of procoagulant and anticoagulant characteristics of this natural lead molecule. Our approach was to investigate the octopus venom protein as a whole or a part of their structure that may result in the development of new lead molecule.

Molecular Modeling and Structural Analysis of Some Snake Venom Specific Toxin Proteins and Cognate Non-Toxin Proteins of Other Chordates.

Protein three-dimensional structures are very much important in terms of functional and evolutionary context. In the present work we evaluated the snake venom constituent cytotoxin, short neurotoxin and related non-toxin proteins of other chordates with reference to structure prediction, validation of the models, distribution of secondary structural elements, hydrophobicity molecular surface analysis, functional annotation and functionally critical binding site identification with the assistance of different bioinformatical tools. Homology models have been generated with the help of Swiss-model and ITASSER suite during the present study. Afterwards the refined structural models were validated with standard methods. For functional annotation of protein molecules we used Protein Information Resource (PIR) database. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) was determined using the COACH program. Structural analysis of snake venom toxin proteins and related non-toxin proteins of other chordates elucidated their structural level conservation of molecular structural surfaces and biophysical characteristics to different extents. Different structural level improvement strategies were observed which are necessary for better system dependent adaptation to diverse biological environment and functional necessities of these protein molecules. Molecular models and their structural characterization of these proteins as documented in this study may provide a valuable aid for drug designing in future.

STRUCTURAL UNDERSTANDING OF CYTOTOXIN 1 OF NAJA SPUTATRIX: A POTENTIAL ANTICANCER AGENT

Snake venom cytotoxin from different Naja species possesses significant cytotoxic activity on tumor cells. The cytoxin from snake venom can exert a plethora of biological activities including depolarization and muscular cell contraction, lysis of variety of cells such as red blood cells, epithelial cells and fetal lung cells, and also apoptotic activity on certain types of tumor cells. In the present article, we have effectively utilized comparative modeling approach to propose the first molecular model structure of cytotoxin 1 of Naja sputatrix . The charge distribution on the structure and distribution of secondary structural elements were also investigated with the aid of In silico based approach. A homology structural model of the protein was generated and analyzed to deduce molecular enrichment strategy. The model data and other relevant post model analysis data provides a clear understanding of molecular structure of cytotoxin 1 of Naja sputatrix and its relevant cytotoxic potential for the development of a beneficial anticancer natural lead compound. Keywords: Cytotoxin 1, Naja Sputatrix, Anticancer Agent, Snake Venom, Structural model, Malayan cobra.

Possible Function of the ribT Gene of Bacillus subtilis: Theoretical Prediction, Cloning, and Expression

The complete decipherment of the functions and interactions of the elements of the riboflavin biosynthesis operon (rib operon) of Bacillus subtilis are necessary for the development of superproducers of this important vitamin. The function of its terminal ribT gene has not been established to date. In this work, a search for homologs of the hypothetical amino acid sequence of the gene product through databases, as well as an analysis of the homolgs, was performed; the distribution of secondary structure elements was theoretically predicted; and the tertiary structure of the RibT protein was proposed. The ribT gene nucleotide sequence was amplified and cloned into the standard high-copy expression vector pET15b and then expressed after induction with IPTG in E. coli BL21 (DE3) strain cells containing the inducible phage T7 RNA polymerase gene. The ribT gene expression was confirmed by SDS-PAGE. The protein product of the expression was purified by affinity chromatography. Therefore, the real possibility of RibT protein production in quantities sufficient for further investigation of its structure and functional activity was demonstrated.

Engineered Symmetric Connectivity of Secondary Structure Elements Highlights Malleability of Protein Folding Pathways

To understand the role of sequence connectivity in protein folding pathways, we explored by Phi-value analysis the folding pathway of an engineered circularly permuted PDZ domain. This variant has the same sequence connectivity as naturally occurring circularly permuted PDZ domains and displays a symmetrical distribution of secondary structure elements (i.e., beta beta alpha beta beta alpha beta beta) while maintaining the same tertiary interactions of the well-characterized second PDZ domain from PTP-BL (PDZ2). Reliable Phi values were obtained for both a low-energy intermediate and the late rate-limiting transition state, allowing a description of both early and late events in folding. A comparison with Phi values obtained for wild-type PDZ2 reveals that while the structure of the late transition state is robust and unaffected by circular permutation, the folding intermediate is stabilized by a different nucleus involving residues located at the new N- and C-termini. The results suggest that folding is driven by competing nuclei whose stabilities may be selectively tuned by circular permutation.

Probing Structural Changes of Proteins Incorporated into Water-in-Oil Emulsions

The applicability of different techniques, that is, Differential Scanning Calorimetry (DSC), Fourier Transform Infrared Spectroscopy (FTIR), and intrinsic tryptophan fluorescence, for probing the structural changes of proteins in the water-in-oil emulsions are investigated using nondefatted bovine (BSA) and human serum albumin (HSA) as model proteins. FTIR shows that the overall secondary structure of the proteins changes to some extent, 12% for BSA and 9% for HSA, when these are incorporated into the emulsion. There was no evidence of changes in the distribution of secondary structural elements apart from the changes in overall secondary structure. A blue shift of 12 to 14 nm in the fluorescence emission maximum was observed for proteins in the emulsion and 3 to 11 nm in the simulated interior of the aqueous phase, thus indicating structural changes around the tryptophan residues. DSC scans indicated that the domains in the proteins change because the shape of the transition peaks changes, when the proteins were incorporated into the emulsions. The total enthalpy decreases for BSA and HSA when these are incorporated into the emulsion, and some changes to the transition temperatures are observed. All the applied techniques supplement each other to give a more complete picture of the structural changes in proteins in intact water-in-oil emulsions. © 2004 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 93:1847–1859, 2004

Preformed Structural Elements Feature in Partner Recognition by Intrinsically Unstructured Proteins

Intrinsically unstructured proteins (IUPs) are devoid of extensive structural order but often display signs of local and limited residual structure. To explain their effective functioning, we reasoned that such residual structure can be crucial in their interactions with their structured partner(s) in a way that preformed structural elements presage their final conformational state. To check this assumption, a database of 24 IUPs with known 3D structures in the bound state has been assembled and the distribution of secondary structure elements and backbone torsion angles have been analysed. The high proportion of residues in coil conformation and with φ, ψ angles in the disallowed regions of the Ramachandran map compared to the reference set of globular proteins shows that IUPs are not fully ordered even in their bound form. To probe the effect of partner proteins on IUP folding, inherent conformational preferences of IUP sequences have been assessed by secondary structure predictions using the GOR, ALB and PROF algorithms. The accuracy of predicting secondary structure elements of IUPs is similar to that of their partner proteins and is significantly higher than the corresponding values for random sequences. We propose that strong conformational preferences mark regions in IUPs (mostly helices), which correspond to their final structural state, while regions with weak conformational preferences represent flexible linkers between them. In our interpretation, preformed elements could serve as initial contact points, the binding of which facilitates the reeling of the flexible regions onto the template. This finding implies that IUPs draw a functional advantage from preformed structural elements, as they enable their facile, kinetically and energetically less demanding, interaction with their physiological partner.

Environmental influences on bovine kappa-casein: reduction and conversion to fibrillar (amyloid) structures.

The caseins of milk form a unique calcium-phosphate transport complex that provides these necessary nutrients to the neonate. The colloidal stability of these particles is primarily the result of kappa-casein. As purified from milk, this protein occurs as spherical particles with a weight average molecular weight of 1.18 million. The protein exhibits a unique disulfide bonding pattern, which (in the absence of reducing agents) ranges from monomer to octamers and above on SDS-PAGE. Severe heat treatment of the kappa-casein (90 degrees C) in the absence of SDS, before electrophoresis, caused an increase in the polymeric distribution: up to 40% randomly aggregated high-molecular weight polymers, presumably promoted by free sulfhydryl groups (J. Protein Chem. 17: 73-84, 1998). To ascertain the role of the sulfhydryl groups, the protein was reduced and carboxymethylated (RCM-K). Surprisingly, at only 37 degrees C, the RCM-kappa-casein exhibited an increase in weight average molecular weight and tendency to self-association when studied at 3000 rpm by analytical ultracentrifugation. Electron microscopy (EM) of the 37 degrees C RCM sample showed that, in addition to the spherical particles found in the native protein, there was a high proportion of fibrillar structures. The fibrillar structures were up to 600 nm in length. Circular dichroism (CD) spectroscopy was used to investigate the temperature-induced changes in the secondary structure of the native and RCM-kappa-caseins. These studies indicate that there was little change in the distribution of secondary structural elements during this transition, with extended strand and beta turns predominating. On the basis of three-dimensional molecular modeling predictions, there may exist a tyrosine-rich repeated sheet-turn-sheet motif in kappa-casein (residues 15-65), which may allow for the stacking of the molecules into fibrillar structures. Previous studies on amyloid proteins have suggested that such motifs promote fibril formation, and near-ultraviolet CD and thioflavin-T binding studies on RCM-kappa-casein support this concept. The results are discussed with respect to the role that such fibrils may play in the synthesis and secretion of casein micelles in lactating mammary gland.

Assessing the impact of secondary structure and solvent accessibility on protein evolution.

Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution-both above and below the species level-will not be well understood until the physical constraints that affect protein evolution are identified and characterized.