scholarly journals “Newton’s cradle” proton relay with amide–imidic acid tautomerization in inverting cellulase visualized by neutron crystallography

2015 ◽  
Vol 1 (7) ◽  
pp. e1500263 ◽  
Author(s):  
Akihiko Nakamura ◽  
Takuya Ishida ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
Shinya Fushinobu ◽  
...  
Keyword(s):  
Glycoside Hydrolases ◽  
Side Chain ◽  
Enzymatic Reactions ◽  
X Ray Diffraction ◽  
Peptide Bonds ◽  
Proton Relay ◽  
Newton’S Cradle ◽  
Dynamics Simulations ◽  
Hydrolysis Of

Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the “Newton’s cradle”–like proton relay pathway of the catalytic cycle. Amide–imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.

scholarly journals Discovery of Stealthin Derivatives and Implication of the Amidotransferase FlsN3 in the Biosynthesis of Nitrogen-Containing Fluostatins

Marine Drugs ◽  
2019 ◽  
Vol 17 (3) ◽  
pp. 150 ◽  
Author(s):  
Chunshuai Huang ◽  
Chunfang Yang ◽  
Zhuangjie Fang ◽  
Liping Zhang ◽  
Wenjun Zhang ◽  
...  
Keyword(s):  
Spectroscopic Data ◽  
Bioinformatics Analysis ◽  
Biological Activities ◽  
Side Chain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Aromatic Polyketides ◽  
Plausible Mechanism ◽  
Encoding Gene

Diazobenzofluorene-containing atypical angucyclines exhibit promising biological activities. Here we report the inactivation of an amidotransferase-encoding gene flsN3 in Micromonospora rosaria SCSIO N160, a producer of fluostatins. Bioinformatics analysis indicated that FlsN3 was involved in the diazo formation. Chemical investigation of the flsN3-inactivation mutant resulted in the isolation of a variety of angucycline aromatic polyketides, including four racemic aminobenzo[b]fluorenes stealthins D–G (9–12) harboring a stealthin C-like core skeleton with an acetone or butanone-like side chain. Their structures were elucidated on the basis of nuclear magnetic resonance (NMR) spectroscopic data and X-ray diffraction analysis. A plausible mechanism for the formation of stealthins D–G (9–12) was proposed. These results suggested a functional role of FlsN3 in the formation/modification of N–N bond-containing fluostatins.

scholarly journals Forging tools for refining predicted protein structures

2019 ◽  
Vol 116 (19) ◽  
pp. 9400-9409 ◽  
Author(s):  
Xingcheng Lin ◽  
Nicholas P. Schafer ◽  
Wei Lu ◽  
Shikai Jin ◽  
Xun Chen ◽  
...  
Keyword(s):  
Protein Structures ◽  
Low Frequency ◽  
Coarse Grained ◽  
Side Chain ◽  
X Ray Diffraction ◽  
Collective Variables ◽  
Coarse Grained Model ◽  
Mechanical Deformations ◽  
Speed Up ◽  
Dynamics Simulations

Refining predicted protein structures with all-atom molecular dynamics simulations is one route to producing, entirely by computational means, structural models of proteins that rival in quality those that are determined by X-ray diffraction experiments. Slow rearrangements within the compact folded state, however, make routine refinement of predicted structures by unrestrained simulations infeasible. In this work, we draw inspiration from the fields of metallurgy and blacksmithing, where practitioners have worked out practical means of controlling equilibration by mechanically deforming their samples. We describe a two-step refinement procedure that involves identifying collective variables for mechanical deformations using a coarse-grained model and then sampling along these deformation modes in all-atom simulations. Identifying those low-frequency collective modes that change the contact map the most proves to be an effective strategy for choosing which deformations to use for sampling. The method is tested on 20 refinement targets from the CASP12 competition and is found to induce large structural rearrangements that drive the structures closer to the experimentally determined structures during relatively short all-atom simulations of 50 ns. By examining the accuracy of side-chain rotamer states in subensembles of structures that have varying degrees of similarity to the experimental structure, we identified the reorientation of aromatic side chains as a step that remains slow even when encouraging global mechanical deformations in the all-atom simulations. Reducing the side-chain rotamer isomerization barriers in the all-atom force field is found to further speed up refinement.

scholarly journals Evolution Rescues Folding of Human Immunodeficiency Virus-1 Envelope Glycoprotein GP120 Lacking a Conserved Disulfide Bond

2008 ◽  
Vol 19 (11) ◽  
pp. 4707-4716 ◽  
Author(s):  
Rogier W. Sanders ◽  
Shang-Te D. Hsu ◽  
Eelco van Anken ◽  
I. Marije Liscaljet ◽  
Martijn Dankers ◽  
...  
Keyword(s):  
Disulfide Bond ◽  
Disulfide Bonds ◽  
Side Chain ◽  
Viral Glycoprotein ◽  
Immunodeficiency Virus ◽  
Glycoprotein Gp120 ◽  
Dynamics Simulations ◽  
Β Sheet

The majority of eukaryotic secretory and membrane proteins contain disulfide bonds, which are strongly conserved within protein families because of their crucial role in folding or function. The exact role of these disulfide bonds during folding is unclear. Using virus-driven evolution we generated a viral glycoprotein variant, which is functional despite the lack of an absolutely conserved disulfide bond that links two antiparallel β-strands in a six-stranded β-barrel. Molecular dynamics simulations revealed that improved hydrogen bonding and side chain packing led to stabilization of the β-barrel fold, implying that β-sheet preference codirects glycoprotein folding in vivo. Our results show that the interactions between two β-strands that are important for the formation and/or integrity of the β-barrel can be supported by either a disulfide bond or β-sheet favoring residues.

scholarly journals Elements in nucleotide sensing and hydrolysis of the AAA+ disaggregation machine ClpB: a structure-based mechanistic dissection of a molecular motor

2014 ◽  
Vol 70 (2) ◽  
pp. 582-595 ◽  
Author(s):  
Cathleen Zeymer ◽  
Thomas R. M. Barends ◽  
Nicolas D. Werbeck ◽  
Ilme Schlichting ◽  
Jochen Reinstein
Keyword(s):  
Atp Hydrolysis ◽  
Mutational Analysis ◽  
Molecular Motor ◽  
Nucleotide Binding ◽  
Side Chain ◽  
Side Chain Conformation ◽  
Proposed Model ◽  
Hydrolysis Of ◽  
Conserved Residue

ATPases of the AAA+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from ATP hydrolysis into mechanical force. This study focuses on the molecular chaperone ClpB, the bacterial homologue of Hsp104, which reactivates aggregated proteins under cellular stress conditions. Based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the ATPase cycle of the C-terminal nucleotide-binding domain (NBD2), one of the motor subunits of this AAA+ disaggregation machine, is dissected mechanistically. The results provide insights into nucleotide sensing, explaining how the conserved sensor 2 motif contributes to the discrimination between ADP and ATP binding. Furthermore, the role of a conserved active-site arginine (Arg621), which controls binding of the essential Mg2+ion, is described. Finally, a hypothesis is presented as to how the ATPase activity is regulated by a conformational switch that involves the essential Walker A lysine. In the proposed model, an unusual side-chain conformation of this highly conserved residue stabilizes a catalytically inactive state, thereby avoiding unnecessary ATP hydrolysis.

scholarly journals Unexpected Enzyme TEM-126: Role of Mutation Asp179Glu

2005 ◽  
Vol 49 (10) ◽  
pp. 4280-4287 ◽  
Author(s):  
J. Delmas ◽  
F. Robin ◽  
F. Bittar ◽  
C. Chanal ◽  
R. Bonnet
Keyword(s):  
Escherichia Coli ◽  
Conformational Changes ◽  
Hydrolytic Activity ◽  
Side Chain ◽  
Omega Loop ◽  
Synergy Test ◽  
Dynamics Simulations ◽  
Apparent Susceptibility ◽  
Level Resistance

ABSTRACT The clinical isolate Escherichia coli CF884 exhibited low-level resistance to ceftazidime (4 μg/ml) by a positive double-disk synergy test and apparent susceptibility to cefuroxime, cefotaxime, cefepime, cefpirome, and aztreonam. The enzyme implicated in this phenotype was a novel 180-kb plasmid-encoded TEM-type extended-spectrum β-lactamase designated TEM-126 which harbors the mutations Asp179Glu and Met182Thr. TEM-126 exhibited significant hydrolytic activity (k cat, 2 s−1) and a Km value of 82 μM against ceftazidime. Molecular dynamics simulations suggested that the substitution Asp179Glu induces subtle conformational changes to the omega loop which may favor the insertion of ceftazidime in the binding site and the correct positioning of the crucial residue Glu166. Overall, these results highlight the remarkable plasticity of TEM enzymes, which can expand their activity against ceftazidime by the addition of one carbon atom in the side chain of residue 179.

scholarly journals Data from molecular dynamics simulations in support of the role of human CES1 in the hydrolysis of Amplex Red

Data in Brief ◽  
2016 ◽  
Vol 6 ◽  
pp. 865-870 ◽  
Author(s):  
Giulio Vistoli ◽  
Achim Treumann ◽  
Thomas von Zglinicki ◽  
Satomi Miwa
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amplex Red ◽  
Dynamics Simulations ◽  
Hydrolysis Of

SYNTHESIS FOR NANOFLOWER AND ROD OF ZnO BY A SURFACTANT FREE AND LOW TEMPERATURE METHOD

2010 ◽  
Vol 17 (02) ◽  
pp. 173-176 ◽  
Author(s):  
BYUNG SUN HAN ◽  
YOUNG RANG UHM ◽  
CHANG KYU RHEE
Keyword(s):  
Acetic Acid ◽  
Morphological Changes ◽  
Distilled Water ◽  
X Ray Diffraction ◽  
Temperature Method ◽  
Diffraction Patterns ◽  
Rapid Hydrolysis ◽  
Zno Powder ◽  
Hydrolysis Of

ZnO with 2D flower-like and 1D rod shape were obtained from simple and rapid hydrolysis of Zn nanopowder. The Zn nanopowders were incorporated into distilled water with acetic acid and then the solution was stirred at 60°C for 8 h. The nanoflower-like and rod shape were formed without any surfactant. It seems that the acetic acid played a role of controlling PH and etching the oxide layer on the surface of metal nanopowders to enhance rapid reaction with distilled water. X-ray diffraction patterns for all samples exhibited that the resultant precipitates were completely transformed to ZnO powder. It is clearly observed that the morphological changes of ZnO with reaction time in aqueous solution follows chestnut bur → flower → tetrahedron → rod sequences during the hydrolysis reaction.

Identification of acid-insoluble filter-plugging compounds and optimal acid-washing procedures for tubular backpulse pressure filters

TAPPI Journal ◽  
2011 ◽  
Vol 10 (1) ◽  
pp. 17-23
Author(s):  
KEVIN TAYLOR ◽  
RICH ADDERLY ◽  
GAVIN BAXTER
Keyword(s):  
Calcium Sulfate ◽  
Membrane Filter ◽  
Sulfamic Acid ◽  
Xrd Analysis ◽  
Metal Sulfides ◽  
X Ray Diffraction ◽  
X Ray ◽  
Gypsum Formation ◽  
Acid Washing ◽  
Hydrolysis Of

Over time, performance of tubular backpulse pressure filters in kraft mills deteriorates, even with regular acid washing. Unscheduled filter replacement due to filter plugging results in significant costs and may result in mill downtime. We identified acid-insoluble filter-plugging materials by scanning electron microscope/energy-dispersion X-ray spectroscopy (SEM/EDS) and X-ray diffraction (XRD) analysis in both polypropylene and Gore-Tex™ membrane filter socks. The major filter-plugging components were calcium sulfate (gypsum), calcium phosphate (hydroxylapatite), aluminosilicate clays, metal sulfides, and carbon. We carried out detailed sample analysis of both the standard acid-washing procedure and a modified procedure. Filter plugging by gypsum and metal sulfides appeared to occur because of the acid-washing procedure. Gypsum formation on the filter resulted from significant hydrolysis of sulfamic acid solution at temperatures greater than 130°F. Modification of the acid-washing procedure greatly reduced the amount of gypsum and addition of a surfactant to the acid reduced wash time and mobilized some of the carbon from the filter. With surfactant, acid washing was 95% complete after 40 min.

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