The Experts below are selected from a list of 5931 Experts worldwide ranked by ideXlab platform
Huan-xiang Zhou - One of the best experts on this subject based on the ideXlab platform.
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liquid liquid phase separation of patchy particles illuminates diverse effects of regulatory components on protein droplet formation
Scientific Reports, 2018Co-Authors: Valery Nguemaha, Huan-xiang ZhouAbstract:Recently many cellular functions have been associated with membraneless organelles, or protein droplets, formed by liquid-liquid phase separation (LLPS). Proteins in these droplets often contain RNA-binding domains, but the effects of RNA on LLPS have been controversial. To gain better understanding on the roles of RNA and other macromolecular regulators, here we used Gibbs-ensemble simulations to determine phase diagrams of two-component patchy particles, as models for mixtures of proteins with regulatory components. Protein-like particles have four patches, with attraction strength ePP; regulatory particles experience mutual Steric Repulsion but have two attractive patches toward proteins, with the strength ePR tunable. At low ePR, the regulator, due to Steric Repulsion, preferentially partitions in the dispersed phase, thereby displacing the protein into the droplet phase and promoting LLPS. At moderate ePR, the regulator starts to partition and displace the protein in the droplet phase, but only to weaken bonding networks and thereby suppress LLPS. At ePR > ePP, the enhanced bonding ability of the regulator initially promotes LLPS, but at higher amounts, the resulting displacement of the protein suppresses LLPS. These results illustrate how RNA can have disparate effects on LLPS, thus able to perform diverse functions in different organelles.
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liquid liquid phase separation of patchy particles illuminates diverse effects of regulatory components on protein droplet formation
bioRxiv, 2018Co-Authors: Valery Nguemaha, Huan-xiang ZhouAbstract:Recently many cellular functions have been associated with membraneless organelles, or protein droplets, formed by liquid-liquid phase separation (LLPS). Proteins in these droplets often contain RNA-binding domains, but the effects of RNA on LLPS have been controversial. To gain better understanding on the roles of RNA, here we used Gibbs-ensemble simulations to determine phase diagrams of two-component patchy particles, as models for mixtures of proteins with RNA or other regulatory components. Protein-like particles have four patches, with attraction strength e PP ; regulatory particles experience mutual Steric Repulsion but have two attractive patches toward proteins, with the strength e PR tunable. At low e PR , the regulator, due to Steric Repulsion, preferentially partitions in the dispersed phase, thereby displacing the protein into the droplet phase and promoting LLPS. At moderate e PR , the regulator starts to partition and displace the protein in the droplet phase, but only to weaken bonding networks and thereby suppress LLPS. At e PR > e PP , the enhanced bonding ability of the regulator initially promotes LLPS, but at higher amounts, the resulting displacement of the protein suppresses LLPS. These results illustrate how RNA can have disparate effects on LLPS, thus able to perform diverse functions in different organelles.
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macromolecular crowding and confinement biochemical biophysical and potential physiological consequences
Annual Review of Biophysics, 2008Co-Authors: Huan-xiang Zhou, German Rivas, Allen P MintonAbstract:Expected and observed effects of volume exclusion on the free en- ergy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Find- ings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macro- molecules over and above Steric Repulsion, are discussed. Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the com- plexity of living organisms are suggested.
Koichi Mikami - One of the best experts on this subject based on the ideXlab platform.
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complete reversal in regioselectivity in the baeyer villiger reaction of an α cf3 ketone and theoretical rationale for axial orientation of Sterically demanding cf3 group at the transition state
Organic Letters, 2003Co-Authors: Yoshimitsu Itoh, Masahiro Yamanaka, Koichi MikamiAbstract:The regioselectivity of the Baeyer−Villiger reaction of α-CF3-ketone is completely reversed from that in α-Feq-ketone. Theoretical study rationalized that the reaction proceeds with the Sterically demanding CF3 group in an axial orientation by strong dipole interaction. The guiding principle that strong dipole interaction can overcome Steric Repulsion as a determining factor not only in regio- but also in stereocontrol is proposed.
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complete reversal in regioselectivity in the baeyer villiger reaction of an alpha cf 3 ketone and theoretical rationale for axial orientation of Sterically demanding cf 3 group at the transition state
Organic Letters, 2003Co-Authors: Yoshimitsu Itoh, Masahiro Yamanaka, Koichi MikamiAbstract:The regioselectivity of the Baeyer−Villiger reaction of α-CF3-ketone is completely reversed from that in α-Feq-ketone. Theoretical study rationalized that the reaction proceeds with the Sterically demanding CF3 group in an axial orientation by strong dipole interaction. The guiding principle that strong dipole interaction can overcome Steric Repulsion as a determining factor not only in regio- but also in stereocontrol is proposed.
Akira Matsuda - One of the best experts on this subject based on the ideXlab platform.
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synthesis of 3 7 anhydro d glycero d ido octitol 1 5 6 trisphosphate as an ip 3 receptor ligand using a radical cyclization reaction with a vinylsilyl tether as the key step conformational restriction strategy using Steric Repulsion between adjacent bulky protecting groups on a pyranose ring
Journal of Organic Chemistry, 2000Co-Authors: Satoshi Shuto, Yumi Yahiro, Satoshi Ichikawa, Akira MatsudaAbstract:3,7-Anhydro-d-glycero-d-ido-octitol 1,5,6-trisphosphate (5) was designed as a novel IP3-receptor ligand having a C-glycosidic structure and was synthesized via a radical cyclization reaction with a temporary connecting vinylsilyl tether as the key step. The phenyl 2-O-dimethylvinylsilyl-3,4,6-tri-O-benzyl-1-seleno-β-d-glucopyranoside (7), in the usual 4C1-conformation, was successively treated with Bu3SnH/AIBN and under Tamao oxidation conditions to give a mixture of five C-glycosidic products. On the other hand, similar successive treatment of the corresponding 3,4-di-O-TBS-protected substrates 13 and 24, which were in an unusual 1C4-conformaion due to the Steric Repulsion between the bulky silyl protecting groups, gave the desired 1α-C-glycosides 18 and 25, respectively, as the major products. Thus, the course of the radical cyclization was effectively controlled by a change in the conformation of the pyranose ring into a 1C4-form due to Steric Repulsion between the adjacent bulky TBS-protecting groups ...
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synthesis of c glycosides via radical cyclization reactions with a vinylsilyl tether control of the reaction course by a change in the conformation of the pyranose ring due to Steric Repulsion between adjacent bulky protecting groups
ChemInform, 1999Co-Authors: Yumi Yahiro, Satoshi Ichikawa, Satoshi Shuto, Akira MatsudaAbstract:Abstract A stereoselective method for introducing a C2-unit at the 1α- and 1β-postions of d -glucose and d -mannose, respectively, via a radical cyclization reaction with vinylsilyl group as a temporary connecting tether, was developed. The radical cyclization of d -glucose substrates was effectively facilitated by a change in the conformation of the pyranose ring into a 1 C 4 -form due to Steric Repulsion between adjacent bulky TBS-protecting groups.
Yoshimitsu Itoh - One of the best experts on this subject based on the ideXlab platform.
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complete reversal in regioselectivity in the baeyer villiger reaction of an α cf3 ketone and theoretical rationale for axial orientation of Sterically demanding cf3 group at the transition state
Organic Letters, 2003Co-Authors: Yoshimitsu Itoh, Masahiro Yamanaka, Koichi MikamiAbstract:The regioselectivity of the Baeyer−Villiger reaction of α-CF3-ketone is completely reversed from that in α-Feq-ketone. Theoretical study rationalized that the reaction proceeds with the Sterically demanding CF3 group in an axial orientation by strong dipole interaction. The guiding principle that strong dipole interaction can overcome Steric Repulsion as a determining factor not only in regio- but also in stereocontrol is proposed.
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complete reversal in regioselectivity in the baeyer villiger reaction of an alpha cf 3 ketone and theoretical rationale for axial orientation of Sterically demanding cf 3 group at the transition state
Organic Letters, 2003Co-Authors: Yoshimitsu Itoh, Masahiro Yamanaka, Koichi MikamiAbstract:The regioselectivity of the Baeyer−Villiger reaction of α-CF3-ketone is completely reversed from that in α-Feq-ketone. Theoretical study rationalized that the reaction proceeds with the Sterically demanding CF3 group in an axial orientation by strong dipole interaction. The guiding principle that strong dipole interaction can overcome Steric Repulsion as a determining factor not only in regio- but also in stereocontrol is proposed.
Xiaofei Zhang - One of the best experts on this subject based on the ideXlab platform.
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density functional theory study of the mechanism of a dipeptide catalyzed intermolecular aldol reaction the effects of Steric Repulsion interactions on stereoselectivity
RSC Advances, 2016Co-Authors: Xiaofei ZhangAbstract:The mechanism of the dipeptide (S)-pro-(S)-asp catalyzed intermolecular aldol reaction with acetone as the donor and three aromatic aldehydes (benzaldehyde, p-methyl benzaldehyde and p-nitrobenzaldehyde) as the acceptors was studied by means of density functional theory (DFT) at the level of B3LYP/6-31G(d,p). The calculated results showed that there were four steps in the reaction path: (i) the nucleophilic attack of an amino group on carbonyl for the formation of intermediate A, which was the rate-determining step due to it having the largest energy barrier of 44.33 kcal mol−1; (ii) the dehydration process to form an s-cis- or s-trans-enamine through an imine-generating step; (iii) the electrophilic addition of aldehyde, which decided the stereoselectivity of the product because of the Steric Repulsion interactions between the enamine and aldehyde; (iv) the removal of the dipeptide to generate the final products. According to the results analysis, it was found that the dipeptide-catalyzed aldol reaction via an s-trans-enamine was more energetically favorable to obtain the R-product (with an ee value > 99%). The energy variations in the reaction path were verified using CAM-B3LYP and M06-2X methods in the same basis set. The solvation effects were explored based on B3LYP/6-31G(d,p) combined with a polarizable continuum model (PCM), the substituent effects of aromatic aldehydes were also considered. The computed results provided a reference for experiments that DMSO and H2O as the solvents could decrease the energy barriers in the reaction path and the impact of substituent effects might be small. The feasibility of the dipeptide provided a possibility for proteins to act as catalysts which are green and nontoxic.
