scholarly journals Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0251751
Author(s):  
Siti Nor Hasmah Ishak ◽  
Nor Hafizah Ahmad Kamarudin ◽  
Mohd Shukuri Mohamad Ali ◽  
Adam Thean Chor Leow ◽  
Fairolniza Mohd Shariff ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Substrate Preference ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Docking Analysis ◽  
Three Dimensional Structure ◽  
Ion Interactions ◽  
The Stability

5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters.

Influence of Cl/Br substitution on the stereochemical peculiarities of copper(I) π-complexes with the 1-allyl-2-aminopyridinium cation

2003 ◽  
Vol 59 (11) ◽  
pp. m478-m481 ◽  
Author(s):  
Evgeny Goreshnik ◽  
Dieter Schollmeier ◽  
Marian Mys'kiv
Keyword(s):  
Hydrogen Bonds ◽  
Electrochemical Synthesis ◽  
Three Dimensional ◽  
Alternating Current ◽  
Dimensional Structure ◽  
Three Dimensional Structure

By using alternating-current electrochemical synthesis, crystals of the CuI π-complexes bis(1-allyl-2-aminopyridinium) di-μ-chloro-bis[chlorocopper(I)], (C8H11N2)2[Cu2Cl4] or [H2NC5H4NC3H5][CuCl2], and bis(1-allyl-2-aminopyridinium) di-μ-(chloro/bromo)-bis[(chloro/bromo)copper(I)], (C8H11N2)2[Cu2Br2.2Cl1.8] or [H2NC5H4NC3H5][CuBr1.10Cl0.90], have been obtained and structurally investigated. In each of the isostructural (isomorphous) compounds, the distorted tetrahedral Cu environment involves three halide atoms and the C=C bond of the ligand. Both compounds reside on inversion centres, and the dimeric [Cu2 X 4·2H2NC5H4NC3H5] units are bonded into a three-dimensional structure by N—H...X hydrogen bonds. The Br content in the terminal X1 position is much higher than that in the bridged X2 site.

scholarly journals Crystal structure of 3-deoxy-3-nitromethyl-1,2;5,6-di-O-isopropylidene-α-D-allofuranose

2016 ◽  
Vol 72 (3) ◽  
pp. 314-317
Author(s):  
Jevgeņija Lugiņina ◽  
Vitālijs Rjabovs ◽  
Dmitrijs Stepanovs
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Compound C

The title compound, C13H21NO7{systematic name: (3aR,5S,6R,6aR)-5-[(R)-2,2-dimethyl-1,3-dioxolan-4-yl]-2,2-dimethyl-6-(nitromethyl)tetrahydrofuro[2,3-d][1,3]dioxole}, consists of a substituted 2,2-dimethyltetrahydrofuro[2,3-d][1,3]dioxolane skeleton. The furanose ringAadopts aoT4conformation. The fused dioxolane ringBand the substituent dioxolane ringCalso have twisted conformations. There are no strong hydrogen bonds in the crystal structure: only weak C—H...O contacts are present, which link the molecules to form a three-dimensional structure.

scholarly journals {(3S,5R)-5-(2,4-Difluorophenyl)-5-[(1H-1,2,4-triazol-1-yl)methyl]tetrahydrofuran-3-yl}methyl 4-methylbenzenesulfonate

IUCrData ◽  
2017 ◽  
Vol 2 (2) ◽  
Author(s):  
Qing-Shuang Ma ◽  
Xiao-Guang Wang ◽  
Lei Xu ◽  
Sun Bin ◽  
Dao-Hong Xia ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Axis Direction ◽  
Envelope Conformation ◽  
Compound C ◽  
Best Fit

In the title compound, C21H21F2N3O4S, the tetrahydrofuran ring adopts an envelope conformation with the β-C atom positioned at the flap. The triazole, difluorophenyl and tolyl rings of the various substituents on the tetrahydrofuran ring are inclined at 77.88 (12), 83.81 (10) and 81.00 (10)°, respectively, to the best-fit mean plane through the five atoms of the tetrahydrofuran ring. In the crystal, weak C—H...O and C—H...F hydrogen bonds link the molecules into a three-dimensional structure, with molecules stacked along thea-axis direction.

scholarly journals (E)-N′-[4-(Dimethylamino)benzylidene]propionohydrazide monohydrate

IUCrData ◽  
2016 ◽  
Vol 1 (10) ◽  
Author(s):  
S. Naveen ◽  
Seranthimata Samshuddin ◽  
Manuel Rodrigues ◽  
Dandavathi Arunkumar ◽  
N. K. Lokanath ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Crystal Water ◽  
Three Dimensional Structure ◽  
Π Interactions ◽  
Compound C

In the title hydrated hydrazine compound, C12H17N3O·H2O, the C=N bond adopts an E conformation. In the crystal, water molecules bridge the hydrazine molecules, via N—H...O and O—H...O hydrogen bonds, forming sheets parallel to the bc plane. There are C—H...π interactions present within the sheets, and further C—H...π interactions link the sheets to form a three-dimensional structure.

scholarly journals Bis(μ2-4-nitrophenolato)bis(4-nitrophenolato)di-μ3-oxido-octaphenyltetratin chloroform sesquisolvate [+ solvate]: a tetranuclear stannoxane

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler
Keyword(s):  
Hydrogen Bonds ◽  
Electron Density ◽  
Three Dimensional ◽  
The Other ◽  
Dimensional Structure ◽  
Coordination Geometry ◽  
Asymmetric Unit ◽  
Acta Cryst ◽  
Complex Molecules ◽  
Three Dimensional Structure

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals Crystal structure of tris(2,2′-bipyridine)cobalt(II) bis(1,1,3,3-tetracyano-2-ethoxypropenide)

2019 ◽  
Vol 75 (2) ◽  
pp. 142-145
Author(s):  
Jamila Benabdallah ◽  
Zouaoui Setifi ◽  
Fatima Setifi ◽  
Habib Boughzala ◽  
Abderrahim Titi
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Three Dimensional ◽  
Distorted Octahedron ◽  
Dimensional Structure ◽  
Cobalt Ion ◽  
Space Group ◽  
Three Dimensional Structure ◽  
Rotation Axes

In the title compound, [Co(C10H8N2)3](C9H5N4O)2, the tris(2,2′-bipyridine)cobalt(II) dication lies across a twofold rotation axes in the space group C2/c. The N atoms of the three bipyridine ligands form a distorted octahedron around the cobalt ion. All the N atoms of the polynitrile 1,1,3,3-tetracyano-2-ethoxypropenide anions participate in C—H...N hydrogen bonds ensuring crystal cohesion and forming a three-dimensional structure. The structure is further stabilized by C—H...π(cation) and anion...π(cation) interactions.

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