Local homology and dimensional full-valuedness

A natural criterion for dimensional full-valuedness of locally compact spaces with finitely generated local homology is given.     

Noncommutative differential geometry on the quantum SU(2), I: An algebraic viewpoint

We compute the cyclic homology of the coordinate ring A(SL_q(2)) of the quantum algebraic group SL _q (2). We observe a degeneration of the noncommutative de Rham complex. The results are also verified from the point of view of Connes' noncommutative differential geometry.     

Engineering cytochrome P-450s

Cytochrome P-450 isozymes represent a critical component of nature’s spectrum of detoxification catalysts that could be exploited for bioremediation. The ethanol-inducible human cytochrome P-450 2E1 serves as a model eukaryotic P-450 that complements the bacterial P-450 cam in dehalogenation and detoxification of environmental pollutants. We explored the construction of novel chimeric P-450s using cytochrome P-450 camC and 2E1 genes. For construction of chimera 1 (478 amino acids, 55.14 kDa), 145 amino acids from the N-terminus of P-450 2E1 protein (493 amino acids, 56.84 kDa) were replaced with 130 amino acids from the N-terminus of P-450 camC protein (415 amino acids, 46.66 kDa). In chimera 2 (525 amino acids, 60.24 kDa) the strategy involves replacement of 28 amino acids in the C-terminus of chimera 1 with 75 amino acids from the C-terminus of P-450 camC gene. Homology models of both the chimeric proteins were developed using SWISS-MODEL based on the known crystal structure of cytochrome P-450 camC, BM-3, 1DT6A, and 2C17A. The models indicated that the proposed heme-binding site was intact, which is inevitable for catalytic activity of cytochrome P-450s. The expression of chimera 1 and 2 genes in Escherichia coli DH5α was evident from light-pink cell pellets, protein band in sodium dodecyl sulfate polyacrylamide gel electrophoresis, and diagnostic carbon monoxide-difference spectra. Our studies show that strategies can be developed to exploit the natural diversity of the P-450 superfamily to generate chimeric biocatalysts that would provide new templates amenable to directed evolution.     

Cyclic homology for schemes

Using hypercohomology, we can extend cyclic homology from algebras to all schemes over a ring . By `extend' we mean that the usual cyclic homology of any commutative algebra agrees with the cyclic homology of its corresponding affine scheme.

     

Comparative Modelling of Organic Anion Transporting Polypeptides: Structural Insights and Comparison of Binding Modes

To better understand the functionality of organic anion transporting polypeptides (OATPs) and to design new ligands, reliable structural data of each OATP is needed. In this work, we used a combination of homology model with molecular dynamics simulations to generate a comprehensive structural dataset, that encompasses a diverse set of OATPs but also their relevant conformations. Our OATP models share a conserved transmembrane helix folding harbouring a druggable binding pocket in the shape of an inner pore. Our simulations suggest that the conserved salt bridges at the extracellular region between residues on TM1 and TM7 might influence the entrance of substrates. Interactions between residues on TM1 and TM4 within OATP1 family shown their importance in transport of substrates. Additionally, in transmembrane (TM) 1/2, a known conserved element, interact with two identified motifs in the TM7 and TM11. Our simulations suggest that TM1/2-TM7 interaction influence the inner pocket accessibility, while TM1/2-TM11 salt bridges control the substrate binding stability.     

Glutamine: fructose-6-phosphate amidotransferase (GFAT): homology modelling and designing of new inhibitors using pharmacophore and docking based hierarchical virtual screening protocol

Glutamine: fructose-6-phosphate amidotransferase (GFAT), also termed GFPT1 and GFAT1, catalyzes the first committed step of the hexosamine biosynthesis pathway in mammals and consequently plays an important role in type 2 diabetes. In the present study, a combination of pharmacophore modelling, homology modelling, and molecular docking analysis was performed to design new glutamine competitive inhibitors of human GFAT, and to investigate important interaction details of inhibitor molecules. A pharmacophore model of GFAT inhibitors was developed, subsequently validated, and utilized for the screening by the PHASE database to identify new molecules. Afterwards, homology modelling was performed to construct the glutamine-binding site of the GFAT protein. The modelled active site was utilized to dock the studied molecules to investigate important receptor-ligand interactions and to scrutinize database-screened molecules on the basis of essential interactions. This systematic in silico protocol helped us to identify new molecules that would be explored for the treatment of type 2 diabetes and its complications.     

人顶体酶三维结构的同源模建及其与KF950的分子对接研究

采用同源模建方法首次构建了人顶体酶的三维结构模型, 模型的可靠性经Ramachandran图和Profile_3D图验证. 采用InsightII/Binding site方法准确定位了人顶体酶的活性位点, 并研究了顶体酶重要功能残基在活性位点的立体分布. 在此基础上, 通过柔性分子对接方法首次阐明了顶体酶高效抑制剂KF950与靶酶活性位点的相互作用模式, 发现特异性的氢键相互作用是KF950产生高抑制活性的重要分子基础. 其研究结果将为合理设计新型顶体酶抑制剂, 寻找男性口服避孕药奠定坚实基础.     

C-spaces and matrix of infinite-dimensionality

We investigate classes (m,n)-C which are intermediate between the class S-wid of weakly infinite-dimensional spaces in the sense of Smirnov and the class S-∞-C of finite C-spaces in the sense of Borst. We find relationships between classes (m₁,n₁)-C and (m₂,n₂)-C. It allows us to construct a matrix of infinite-dimensionality.     

Cohen–Macaulayness of monomial ideals and symbolic powers of Stanley–Reisner ideals

We present criteria for the Cohen–Macaulayness of a monomial ideal in terms of its primary decomposition. These criteria allow us to use tools of graph theory and of linear programming to study the Cohen–Macaulayness of monomial ideals which are intersections of prime ideal powers. We can characterize the Cohen–Macaulayness of the second symbolic power or of all symbolic powers of a Stanley–Reisner ideal in terms of the simplicial complex. These characterizations show that the simplicial complex must be very compact if some symbolic power is Cohen–Macaulay. In particular, all symbolic powers are Cohen–Macaulay if and only if the simplicial complex is a matroid complex. We also prove that the Cohen–Macaulayness can pass from a symbolic power to another symbolic powers in different ways.