A new insight into the reaction behaviors of side-chain alkylation of toluene with methanol over CsX

2018 ◽  
Vol 8 (13) ◽  
pp. 3346-3356 ◽  
Author(s):  
Peidong Li ◽  
Qiao Han ◽  
Xiaomin Zhang ◽  
Yangyang Yuan ◽  
Yanfei Zhang ◽  
...  
Keyword(s):  
Side Chain ◽  
Crucial Step ◽  
Styrene Production ◽  
Formation Paths ◽  
Insight Into

The crucial step for styrene production and the formation paths for the main side-products in the side-chain alkylation of toluene with methanol over CsX were unveiled.

A computational insight into the relationship between side chain IR line shapes and local environment in fibril-like structures

2021 ◽  
Vol 154 (8) ◽  
pp. 084105
Author(s):  
Sandra M. V. Pinto ◽  
Nicola Tasinato ◽  
Vincenzo Barone ◽  
Laura Zanetti-Polzi ◽  
Isabella Daidone
Keyword(s):  
Local Environment ◽  
Side Chain ◽  
Line Shapes ◽  
The Relationship ◽  
Insight Into

scholarly journals Corrigendum: Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion

2012 ◽  
Vol 51 (40) ◽  
pp. 9959-9959
Author(s):  
Paul Schanda ◽  
Matthias Huber ◽  
Jérôme Boisbouvier ◽  
Beat H. Meier ◽  
Matthias Ernst
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Dipolar Couplings ◽  
Side Chain ◽  
Side Chain Motion ◽  
Insight Into

scholarly journals Structure of a Talaromyces pinophilus GH62 arabinofuranosidase in complex with AraDNJ at 1.25 Å resolution

2018 ◽  
Vol 74 (8) ◽  
pp. 490-495 ◽  
Author(s):  
Olga V. Moroz ◽  
Lukasz F. Sobala ◽  
Elena Blagova ◽  
Travis Coyle ◽  
Wei Peng ◽  
...  
Keyword(s):  
Plant Biomass ◽  
Cellulosic Biomass ◽  
Structural Basis ◽  
Side Chain ◽  
Polymeric Substrates ◽  
Hydrolysis Of ◽  
Insight Into ◽  
Positively Charged ◽  
Talaromyces Pinophilus ◽  
Resolution Structure

The enzymatic hydrolysis of complex plant biomass is a major societal goal of the 21st century in order to deliver renewable energy from nonpetroleum and nonfood sources. One of the major problems in many industrial processes, including the production of second-generation biofuels from lignocellulose, is the presence of `hemicelluloses' such as xylans which block access to the cellulosic biomass. Xylans, with a polymeric β-1,4-xylose backbone, are frequently decorated with acetyl, glucuronyl and arabinofuranosyl `side-chain' substituents, all of which need to be removed for complete degradation of the xylan. As such, there is interest in side-chain-cleaving enzymes and their action on polymeric substrates. Here, the 1.25 Å resolution structure of the Talaromyces pinophilus arabinofuranosidase in complex with the inhibitor AraDNJ, which binds with a K d of 24 ± 0.4 µM, is reported. Positively charged iminosugars are generally considered to be potent inhibitors of retaining glycosidases by virtue of their ability to interact with both acid/base and nucleophilic carboxylates. Here, AraDNJ shows good inhibition of an inverting enzyme, allowing further insight into the structural basis for arabinoxylan recognition and degradation.

Comparative study of dG affinity vs. DNA methylation modulating properties of side chain derivatives of procainamide: insight into its DNA hypomethylating effect

RSC Advances ◽  
2016 ◽  
Vol 6 (7) ◽  
pp. 5350-5358 ◽  
Author(s):  
R. L. Gawade ◽  
D. K. Chakravarty ◽  
J. Debgupta ◽  
E. Sangtani ◽  
S. Narwade ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Comparative Study ◽  
Structural Features ◽  
Side Chain ◽  
Side Chains ◽  
Hypomethylating Agents ◽  
Derivatives Of ◽  
Insight Into

Structural features of side-chains govern the association of procainamide and its derivatives with dG base of CpG rich DNA, which may differentially hinder the activity of DNMT-1, thereby they act as DNA hypomethylating agents.

Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion

2011 ◽  
Vol 50 (46) ◽  
pp. 11005-11009 ◽  
Author(s):  
Paul Schanda ◽  
Matthias Huber ◽  
Jérôme Boisbouvier ◽  
Beat H. Meier ◽  
Matthias Ernst
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Dipolar Couplings ◽  
Side Chain ◽  
Side Chain Motion ◽  
Insight Into

scholarly journals The X-Ray Structure of the Haloalcohol Dehalogenase HheA from Arthrobacter sp. Strain AD2: Insight into Enantioselectivity and Halide Binding in the Haloalcohol Dehalogenase Family

2006 ◽  
Vol 188 (11) ◽  
pp. 4051-4056 ◽  
Author(s):  
René M. de Jong ◽  
Kor H. Kalk ◽  
Lixia Tang ◽  
Dick B. Janssen ◽  
Bauke W. Dijkstra
Keyword(s):  
Tertiary Structure ◽  
Halogen Bond ◽  
Environmental Pollutants ◽  
Binding Pocket ◽  
Catalytic Triad ◽  
Side Chain ◽  
Structural Determinants ◽  
Substrate Binding Pocket ◽  
X Ray ◽  
Insight Into

ABSTRACT Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which are recalcitrant environmental pollutants. They use a conserved Ser-Tyr-Arg catalytic triad to deprotonate the haloalcohol oxygen, which attacks the halogen-bearing carbon atom, producing an epoxide and a halide ion. Here, we present the X-ray structure of the haloalcohol dehalogenase HheAAD2 from Arthrobacter sp. strain AD2 at 2.0-Å resolution. Comparison with the previously reported structure of the 34% identical enantioselective haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 shows that HheAAD2 has a similar quaternary and tertiary structure but a much more open substrate-binding pocket. Docking experiments reveal that HheAAD2 can bind both enantiomers of the haloalcohol substrate 1-p-nitrophenyl-2-chloroethanol in a productive way, which explains the low enantiopreference of HheAAD2. Other differences are found in the halide-binding site, where the side chain amino group of Asn182 is in a position to stabilize the halogen atom or halide ion in HheAAD2, in contrast to HheC, where a water molecule has taken over this role. These results broaden the insight into the structural determinants that govern reactivity and selectivity in the haloalcohol dehalogenase family.

scholarly journals Inside Cover: Solid-State NMR Measurements of Asymmetric Dipolar Couplings Provide Insight into Protein Side-Chain Motion (Angew. Chem. Int. Ed. 46/2011)

2011 ◽  
Vol 50 (46) ◽  
pp. 10736-10736
Author(s):  
Paul Schanda ◽  
Matthias Huber ◽  
Jérôme Boisbouvier ◽  
Beat H. Meier ◽  
Matthias Ernst
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Dipolar Couplings ◽  
Side Chain ◽  
Side Chain Motion ◽  
Insight Into

scholarly journals pH-Induced Conformational Changes of Human Bocavirus Capsids

2021 ◽  
Author(s):  
Mengxiao Luo ◽  
Mario Mietzsch ◽  
Paul Chipman ◽  
Kangkang Song ◽  
Chen Xu ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Control Strategies ◽  
Variable Region ◽  
Side Chain ◽  
Tissue Tropism ◽  
Human Bocavirus ◽  
Gastrointestinal Infections ◽  
Binding Characteristics ◽  
N Terminus ◽  
Insight Into

Human bocavirus 1 (HBoV1) and HBoV2-4 infect children and immunocompromised individuals, resulting in respiratory and gastrointestinal infections, respectively. Using cryo-electron microscopy and image reconstruction, the HBoV2 capsid structure was determined to 2.7 Å resolution at pH 7.4 and compared to the previously determined HBoV1, HBoV3, and HBoV4 structures. Consistent with previous findings, surface variable region (VR) III of the capsid protein VP3, proposed as a host tissue-tropism determinant, was structurally similar among the gastrointestinal strains HBoV2-4, but differed from HBoV1 with its tropism for the respiratory tract. Towards understanding the entry and trafficking properties of these viruses, HBoV1 and HBoV2 were further analyzed as species representatives of the two HBoV tropisms. Their cell surface glycan-binding characteristics were analyzed, and capsid structures determined to 2.5-2.7 Å resolution at pH 5.5 and 2.6, conditions normally encountered during infection. The data showed that glycans with terminal sialic acid, galactose, GlcNAc or heparan sulfate moieties do not facilitate HBoV1 or HBoV2 cellular attachment. With respect to trafficking, conformational changes common to both viruses were observed at low pH conditions localized to the VP N-terminus under the 5-fold channel, in the surface loops VR-I and VR-V and specific side-chain residues such as cysteines and histidines. The 5-fold conformational movements provide insight into the potential mechanism of VP N-terminal dynamics during HBoV infection and side-chain modifications highlight pH-sensitive regions of the capsid. IMPORTANCE Human bocaviruses (HBoVs) are associated with disease in humans. However, the lack of an animal model and a versatile cell culture system to study their life cycle limits the ability to develop specific treatments or vaccines. This study presents the structure of HBoV2, at 2.7 Å resolution, determined for comparison to the existing HBoV1, HBoV3, and HBoV4 structures, to enable the molecular characterization of strain and genus-specific capsid features contributing to tissue tropism and antigenicity. Furthermore, HBoV1 and HBoV2 structures determined under acidic conditions provide insight into capsid changes associated with endosomal and gastrointestinal acidification. Structural rearrangements of the capsid VP N-terminus, at the base of the 5-fold channel, demonstrate a disordering of a “basket” motif as pH decreases. These observations begin to unravel the molecular mechanism of HBoV infection and provide information for control strategies.

scholarly journals Molecular Dynamics Insight into the Lipid II Recognition by Type A Lantibiotics: Nisin, Epidermin, and Gallidermin

Micromachines ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1169
Author(s):  
Irina Panina ◽  
Amir Taldaev ◽  
Roman Efremov ◽  
Anton Chugunov
Keyword(s):  
Molecular Dynamics ◽  
Side Chain ◽  
Amino Acid Residues ◽  
Simultaneous Formation ◽  
Lipid Ii ◽  
Target Binding ◽  
Dynamics Simulations ◽  
Similar Conformation ◽  
Insight Into

Lanthionine-containing peptides (lantibiotics) have been considered as pharmaceutical candidates for decades, although their clinical application has been restricted. Most lantibiotics kill bacteria via targeting and segregating of the cell wall precursor—membrane-inserted lipid II molecule—in some cases accompanied by pores formation. Nisin-like lantibiotics specifically bind to pyrophosphate (PPi) moiety of lipid II with their structurally similar N-terminal thioether rings A and B. Although possessing higher pore-forming capability, nisin, in some cases, is 10-fold less efficient in vivo as compared to related epidermin and gallidermin peptides, differing just in a few amino acid residues within their target-binding regions. Here, using molecular dynamics simulations, we investigated atomistic details of intermolecular interactions between the truncated analogues of these peptides (residues 1–12) and lipid II mimic (dimethyl pyrophosphate, DMPPi). The peptides adopt similar conformation upon DMPPi binding with backbone amide protons orienting into a single center capturing PPi moiety via simultaneous formation of up to seven hydrogen bonds. Epidermin and gallidermin adopt the complex-forming conformation twice as frequent as nisin does, enhancing the binding by the lysine 4 side chain. Introduction of the similar residue to nisin in silico improves the binding, providing ideas for further design of prototypic antibiotics.

scholarly journals Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects

2019 ◽  
Vol 17 (5) ◽  
pp. 1081-1089 ◽  
Author(s):  
Rohit Kumar ◽  
Kristoffer Peterson ◽  
Majda Misini Ignjatović ◽  
Hakon Leffler ◽  
Ulf Ryde ◽  
...  
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Binding Sites ◽  
Binding Pocket ◽  
Side Chain ◽  
Complex Interplay ◽  
Protein Binding Sites ◽  
Arginine Side Chain ◽  
Galectin 3 ◽  
Insight Into

Analysis of a ligand induced-aglycone-binding pocket in galectin-3 provides detailed insight into interactions of fluorinated phenyl moieties with arginine-containing protein binding sites and the complex interplay of different energetic components in defining the binding affinity.

Sign in / Sign up

Export Citation Format

Share Document