The Experts below are selected from a list of 18 Experts worldwide ranked by ideXlab platform
Kuochen Chou - One of the best experts on this subject based on the ideXlab platform.
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energy optimized structure of antifreeze protein and its binding mechanism
Journal of Molecular Biology, 1992Co-Authors: Kuochen ChouAbstract:Abstract A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine Residues, i.e. Thr2, Thr13, Thr24, Thr35, are aligned on almost the same line parallel to the helix axis and separated successively by 16·1, 16·0 and 16·2 A, respectively, very close to the 16·6 A repeat spacing along [0112] in ice. Based on such a space match, a zipper-like model is proposed to elucidate the binding mechanism of the antifreeze protein to ice crystals. According to the current model, the antifreeze protein may bind to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of these four Thr Residues to the oxygen atoms along the [0112] direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point. The calculated results and the binding mechanism thus derived accord with recent experimental observations. The mechanistic implications derived from such a special antifreeze molecule might be generally applied to elucidate the structure-function relationship of other antifreeze proteins with the following two common features: (1) recurrence of a Thr Residue (or any other polar amino acid Residue whose side-chain can form a hydrogen bond with water) in an 11-amino-acid period along the sequence concerned; and (2) a high percentage of Ala Residue Component therein. Further experiments are suggested to test the ice binding model.
Rommie E Amaro - One of the best experts on this subject based on the ideXlab platform.
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exploring Residue Component contributions to dynamical network models of allostery
Journal of Chemical Theory and Computation, 2012Co-Authors: Adam T Vanwart, John Eargle, Zaida Lutheyschulten, Rommie E AmaroAbstract:Allosteric regulation in biological systems is of considerable interest given the vast number of proteins that exhibit such behavior. Network models obtained from molecular dynamics simulations have been shown to be powerful tools for the analysis of allostery. In this work, different coarse-grain Residue representations (nodes) are used together with a dynamical network model to investigate models of allosteric regulation. This model assumes that allosteric signals are dependent on positional correlations of protein substituents, as determined through molecular dynamics simulations, and uses correlated motion to generate a signaling weight between two given nodes. We examine four types of network models using different node representations in Cartesian coordinates: the (i) Residue α-carbons, (ii) the side chain center of mass, (iii) the backbone center of mass, and the entire (iv) Residue center of mass. All correlations are filtered by a dynamic contact map that defines the allowable interactions betwee...
Christopher J Brandl - One of the best experts on this subject based on the ideXlab platform.
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genetic evidence links the astra protein chaperone Component tti2 to the saga transcription factor tra1
Genetics, 2012Co-Authors: Julie Genereaux, Stephanie Kvas, Dominik Dobransky, Jim Karagiannis, Gregory B Gloor, Christopher J BrandlAbstract:Tra1 is a 3744-Residue Component of the Saccharomyces cerevisiae SAGA, NuA4, and ASTRA complexes. Tra1 contains essential C-terminal PI3K and FATC domains, but unlike other PIKK (phosphoinositide three-kinase–related kinase) family members, lacks kinase activity. To analyze functions of the FATC domain, we selected for suppressors of tra1-F3744A, an allele that results in slow growth under numerous conditions of stress. Two alleles of TTI2, tti2-F328S and tti2-I336F, acted in a partially dominant fashion to suppress the growth-related phenotypes associated with tra1-F3744A as well as its resulting defects in transcription. tti2-F328S suppressed an additional FATC domain mutation (tra1-L3733A), but not a mutation in the PI3K domain or deletions of SAGA or NuA4 Components. We find eGFP-tagged Tti2 distributed throughout the cell. Tti2 is a Component of the ASTRA complex, and in mammalian cells associates with molecular chaperones in complex with Tti1 and Tel2. Consistent with this finding, Tra1 levels are reduced in a strain with a temperature-sensitive allele of tel2. Further agreeing with a possible role for Tti2 in the folding or stabilization of Tra1, tra1-F3744A was mislocalized to the cytoplasm, particularly under conditions of stress. Since an intragenic mutation of tra1-R3590I also suppressed F3744A, we propose that Tti2 is required for the folding/stability of the C-terminal FATC and PI3K domains of Tra1 into their functionally active form.
Adam T Vanwart - One of the best experts on this subject based on the ideXlab platform.
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exploring Residue Component contributions to dynamical network models of allostery
Journal of Chemical Theory and Computation, 2012Co-Authors: Adam T Vanwart, John Eargle, Zaida Lutheyschulten, Rommie E AmaroAbstract:Allosteric regulation in biological systems is of considerable interest given the vast number of proteins that exhibit such behavior. Network models obtained from molecular dynamics simulations have been shown to be powerful tools for the analysis of allostery. In this work, different coarse-grain Residue representations (nodes) are used together with a dynamical network model to investigate models of allosteric regulation. This model assumes that allosteric signals are dependent on positional correlations of protein substituents, as determined through molecular dynamics simulations, and uses correlated motion to generate a signaling weight between two given nodes. We examine four types of network models using different node representations in Cartesian coordinates: the (i) Residue α-carbons, (ii) the side chain center of mass, (iii) the backbone center of mass, and the entire (iv) Residue center of mass. All correlations are filtered by a dynamic contact map that defines the allowable interactions betwee...
Krivtsova Nadejda - One of the best experts on this subject based on the ideXlab platform.
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Heat Treatment Condition Influence on Novokuibyshevsk Vacuum Residue Component Composition
Procedia Chemistry, 2014Co-Authors: Karpov Yury, Krivonosova Anastasia, Krivtsov Evgenii, Golovko Anatolii, Krivtsova NadejdaAbstract:The article presents the information about thermal degradation of Novokuibyshevsk vacuum Residue and change of products composition during this process. The optimal conditions for the thermal destruction of vacuum Residue Components were established. The regularities of material balance composition change, Sgeneral were determined depending on cracking conditions. The basic directions of resin-asphaltene Component transformations were identified, changes in their structural-group parameters in the process of initiated cracking were analyzed. Conducting of Novokuibyshevsk vacuum Residue thermolysis leads to deep resins-asphaltenes average molecules structure characteristic changes. Developed alkyl and naphthenic moieties, which are presented in initial molecule, undergo degradation, amount of structural blocks in resins and asphaltenes molecules reduces, their average size decreases. Also the reduction in total content of the rings (saturated and aromatic) was established in average structural unit, at the same time decrease of rings substitution and length of the aliphatic fragments can be observed. In general the process of vacuum Residue thermal cracking causes partial degradation of saturated (aliphatic and naphthenic) fragments and, partially, aromatic rings, which contain heteroatomic elements.