An evaluation of molecular models of the cytochrome P450 Streptomyces griseolus enzymes P450SU1 and P450SU2

Summary P450SU1 and P450SU2 are herbicide-inducible bacterial cytochrome P450 enzymes from Streptomyces griseolus. They have two of the highest sequence identities to camphor hydroxylase (P450cam from Pseudomonas putida), the cytochrome P450 with the first known crystal structure. We have built several models of these two proteins to investigate the variability in the structures that can occur from using different modeling protocols. We looked at variability due to alignment methods, backbone loop conformations and refinement methods. We have constructed two models for each protein using two alignment algorithms, and then an additional model using an identical alignment but different loop conformations for both buried and surface loops. The alignments used to build the models were created using the Needleman-Wunsch method, adapted for multiple sequences, and a manual method that utilized both a dotmatrix search matrix and the Needleman-Wunsch method. After constructing the initial models, several energy minimization methods were used to explore the variability in the final models caused by the choice of minimization techniques. Features of cytochrome P450cam and the cytochrome P450 superfamily, such as the ferredoxin binding site, the heme binding site and the substrate binding site were used to evaluate the validity of the models. Although the final structures were very similar between the models with different alignments, active-site residues were found to be dependent on the conformations of buried loops and early stages of energy minimization. We show which regions of the active site are the most dependent on the particular methods used, and which parts of the structures seem to be independent of the methods.     

A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building

Summary A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching -helices (C, D, G, I, J, K and L) and -sheets (3/4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, -helices B, B and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val³⁷⁰, Pro³⁷¹, Leu³⁷², Trp³¹⁶, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp¹⁰⁰ or Asp³⁰¹ was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates. These findings are in accordance with a recently published predictive model for substrates of P450 2D6 [Koymans et al., Chem. Res. Toxicol., 5 (1992) 211].     

Optimal lower eigenvalue estimates for Hodge-Laplacian and applications

We consider the eigenvalue problem for Hodge-Laplacian on a Riemannian manifold M isometrically immersed into another Riemannian manifold $\overline{M}$. We first assume the pull back Weitzenböck operator of $\overline{M}$ bounded from below, and obtain an extrinsic lower bound for the first eigenvalue of Hodge-Laplacian. As applications, we obtain some rigidity results. Second, when the pull back Weitzenböck operator of $\overline{M}$ bounded from both sides, we give a lower bound of the first eigenvalue by the Ricci curvature of M and some extrinsic geometry. As a consequence, we prove a weak Ejiri type theorem, that is, if the Ricci curvature bounded from below pointwisely by a function of the norm square of the mean curvature vector, then M is a homology sphere. In the end, we give an example to show that all the eigenvalue estimates are optimal when $\overline{M}$ is the space form.     

Modeling,stability and the activity assessment of glutathione reductase from Streptococcus Thermophilus; Insights from the in-silico simulation study

Antioxidant enzymes (AEs) are the main parts of the natural barriers of the body which deactivate the oxidant factors. To discover and understand their structures and function will deserve a deeper investigation. Accordingly, as an AE of probiotic strains, glutathione reductase of Streptococcus thermophilus (GRst), is characterized and modeled by in-silico methods. The investigation indicated the physicochemical properties of the enzyme and estimated its half-life of being more than 10 h. The analysis revealed that the enzyme is composed of 86 strands, 123 helices, and 241 random coils. Homology modeling of the GRst led to the construction of the enzyme’s 3D model that 62% of which is analogous to the glutathione reductase of Escherichia Coli (GRec), and which is qualitatively high in terms of Molpdf, ERRAT, Verify-3D and Ramachandran scores. Moreover, the structural stability of the model was substantiated within 10 and 20 ns at 400 and 300 K, respectively. Interestingly, these data showed that the enzyme is more stable than GRec at 400 K. In other words, the active cavity of the constructed model is characteristic of 38 amino acid residues within 4 Å around the NADPH and GSSG as corresponding ligands of GRst. Noteworthy, herein is the fact that, CYS40 and CYS45 are specified as the active site residues of this enzyme. Furthermore, the interaction assays of the model support its antioxidant capability which is even more than that of GRec.In general, these data provide a new model of AEs being inclusive of high antioxidant capacity and thermostability.     

Modification of PAE-degrading Esterase(CarEW) for Higher Degradation Efficiency Through Integrated Homology Modeling,Molecular Docking,and Molecular Dynamics Simulation

Six phthalate acid esters(PAEs) priority pollutants[dimethyl phthalate(DMP), diethyl phthalate(DEP), dibutyl phthalate (DBP or DNBP), di-n-octyl phthalate(DNOP), di 2-ethyl hexyl phthalate(DEHP), and butyl benzyl phthalate(BBP)] were opted as the research object. PAE-degrading esterase CarEW(PDB ID:1C7I) isolated from Bacillus subtilis acting as a template and an iterative saturation mutation strategy was adopted to modify key amino acids to attain efficient PAE-degrading esterase substitutes with a reasonable structure constructed by homology modeling method. Present study designed a total of 285 unit-site and multi-site substitutions of PAE-degrading esterase using the homology modeling method. Among them, 207 PAE-degrading esterase substitutions, which contained the 6-site PAE-degrading esterase substitute 1C7I-6-9 with 84.21% enhancement intensity of degradation ability revealed better degradability to all the 6 PAEs after modification. Moreover, molecular dynamics simulation based on the Taguchi method reported the optimal external application environment for PAE-degrading esterase substitutes as follows:pH=6, T=35℃, the rhamnolipid concentration was 50 mg/L, the molar ratio of nitrogen to phosphorus(N:P) was 10:1, the concentration of H₂O₂ was 50 mg/L, and the voltage gradient was 1.5 V/cm. The degradation ability of PAE-degrading esterase substitutes was found to be elevated by 13.04% as compared to that of the blank control under the optimal condition. Moreover, 11 highly efficient PAE-degrading esterase substitutes with thermal stability were designed.     

人3型腺病毒六邻体蛋白同源建模及其进化轨迹分析

用同源建模方法构建了人3型腺病毒六邻体完整的空间结构, 对此结构模型的合理性进行检验, 并通过基于多重序列比对的进化轨迹分析发现, 不同型别的人腺病毒六邻体型特异性序列主要存在于六邻体的塔区上, 结合二级结构分析, 预测位于六邻体塔区表面的几个环区是型特异性中和表位的所在区域.     

S~1 × S~1-Borsuk-Ulam Theorem on Product Spaces

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Homology manifold bordism

The Bryant-Ferry-Mio-Weinberger surgery exact sequence for compact homology manifolds of dimension is used to obtain transversality, splitting and bordism results for homology manifolds, generalizing previous work of Johnston.

First, we establish homology manifold transversality for submanifolds of dimension : if is a map from an -dimensional homology manifold to a space , and is a subspace with a topological -block bundle neighborhood, and , then is homology manifold -cobordant to a map which is transverse to , with an -dimensional homology submanifold.

Second, we obtain a codimension splitting obstruction in the Wall -group for a simple homotopy equivalence from an -dimensional homology manifold to an -dimensional Poincaré space with a codimension Poincaré subspace with a topological normal bundle, such that if (and for only if) splits at up to homology manifold -cobordism.

Third, we obtain the multiplicative structure of the homology manifold bordism groups .

     

Distributive Products and Their Homology

We develop a theory of sets with distributive products (called shelves and multi-shelves) and of their homology. We relate the shelf homology to the rack and quandle homology.