scholarly journals Localising individual atoms of tryptophan side chains in the metallo-<i>β</i>-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

2022 ◽  
Vol 3 (1) ◽  
pp. 1-13
Author(s):  
Henry W. Orton ◽  
Iresha D. Herath ◽  
Ansis Maleckis ◽  
Shereen Jabar ◽  
Monika Szabo ◽  
...  
Keyword(s):  
Active Site ◽  
Side Chains ◽  
Pseudocontact Shifts ◽  
Magnetic Susceptibility Anisotropy ◽  
Single Crystal Structures ◽  
Flexible Loop ◽  
Backbone Amide ◽  
Tryptophan Residues ◽  
Atomic Coordinates ◽  
Tryptophan Side Chains

Abstract. The metallo-β-lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δχ) tensors were determined by measuring pseudocontact shifts (PCSs) of backbone amide protons. The Δχ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.

scholarly journals Localising individual atoms of tryptophan side chains in the metallo-β-lactamase IMP-1 by pseudocontact shifts from paramagnetic lanthanoid tags at multiple sites

2021 ◽  
Author(s):  
Henry W. Orton ◽  
Iresha D. Herath ◽  
Ansis Maleckis ◽  
Shereen Jabar ◽  
Monika Szabo ◽  
...  
Keyword(s):  
Active Site ◽  
Side Chains ◽  
Pseudocontact Shifts ◽  
Magnetic Susceptibility Anisotropy ◽  
Single Crystal Structures ◽  
Flexible Loop ◽  
Backbone Amide ◽  
Tryptophan Residues ◽  
Atomic Coordinates ◽  
Tryptophan Side Chains

Abstract. The metallo-β-lactamase IMP-1 features a flexible loop near the active site that assumes different conformations in single crystal structures, which may assist in substrate binding and enzymatic activity. To probe the position of this loop, we labelled the tryptophan residues of IMP-1 with 7-13C-indole and the protein with lanthanoid tags at three different sites. The magnetic susceptibility anisotropy (Δχ) tensors were determined by measuring pseudocontact shifts (PCS) of backbone amide protons. The Δχ tensors were subsequently used to identify the atomic coordinates of the tryptophan side chains in the protein. The PCSs were sufficient to determine the location of Trp28, which is located in the active site loop targeted by our experiments, with high accuracy. Its average atomic coordinates showed barely significant changes in response to the inhibitor captopril. It was found that localisation spaces could be defined with better accuracy by including only the PCSs of a single paramagnetic lanthanoid ion for each tag and tagging site. The effect was attributed to the shallow angle with which PCS isosurfaces tend to intersect if generated by tags and tagging sites that are identical except for the paramagnetic lanthanoid ion.

Studies on the tryptophan residues of soybean agglutinin. Involvement in saccharide binding

1989 ◽  
Vol 9 (2) ◽  
pp. 189-198 ◽  
Author(s):  
Musti Joginadha Swamy ◽  
Avadhesha Surolia
Keyword(s):  
Active Site ◽  
Blue Shift ◽  
Binding Activity ◽  
Carbohydrate Binding ◽  
Side Chains ◽  
Soybean Agglutinin ◽  
Protein Fluorescence ◽  
Saccharide Binding ◽  
Tryptophan Residues ◽  
Tryptophan Side Chains

Modification of tryptophan side chains of soybean agglutinin (SBA) with N-bromosuccinimide results in a loss of the hemagglutinating and carbohydrate binding activities of the protein. One residue/subunit is probably essential for the binding activity. Modification leads to a large decrease in the fluorescene of the protein accompained by a blue shift. Iodide ion quenching of the protein fluorescence shows that saccharide binding results in a decreased accessibility of some of the tryptophan side chains. These results strongly point towards the involvement of tryptophan residues in the active site of SBA.

scholarly journals Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase

ACS Catalysis ◽  
2020 ◽  
Vol 10 (19) ◽  
pp. 11253-11267
Author(s):  
Anil R. Mhashal ◽  
Adrian Romero-Rivera ◽  
Lisa S. Mydy ◽  
Judith R. Cristobal ◽  
Andrew M. Gulick ◽  
...  
Keyword(s):  
Active Site ◽  
Hydride Transfer ◽  
Side Chains ◽  
Flexible Loop ◽  
Glycerol 3 Phosphate Dehydrogenase

Studies on a Tyr residue critical for the binding of coenzyme and substrate in mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21): structure of the Y224D mutant enzyme

2010 ◽  
Vol 66 (2) ◽  
pp. 198-204
Author(s):  
Urmi Dhagat ◽  
Satoshi Endo ◽  
Hiroaki Mamiya ◽  
Akira Hara ◽  
Ossama El-Kabbani
Keyword(s):  
Crystal Structure ◽  
Active Site ◽  
Unique Feature ◽  
Hydroxysteroid Dehydrogenase ◽  
Kinetic Constants ◽  
Mutant Enzyme ◽  
Side Chains ◽  
Wild Type ◽  
Stereospecific Reduction ◽  
Flexible Loop

Mouse 3(17)α-hydroxysteroid dehydrogenase (AKR1C21) is the only aldo–keto reductase that catalyzes the stereospecific reduction of 3- and 17-ketosteroids to the corresponding 3(17)α-hydroxysteroids. The Y224D mutation of AKR1C21 reduced theKmvalue for NADP(H) by up to 80-fold and completely reversed the 17α stereospecificity of the enzyme. The crystal structure of the Y224D mutant at 2.3 Å resolution revealed that the mutation resulted in a change in the conformation of the flexible loop B, including the V-shaped groove, which is a unique feature of the active-site architecture of wild-type AKR1C21 and is formed by the side chains of Tyr224 and Trp227. Furthermore, mutations (Y224F and Q222N) of residues involved in forming the safety belt for binding of the coenzyme showed similar alterations in kinetic constants for 3α-hydroxy/3-ketosteroids and 17-hydroxy/ketosteroids compared with the wild type.

scholarly journals Uncovering the Role of Key Active Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalysed by Wild-Type and Variants of Triosephosphate Isomerase

2019 ◽  
Author(s):  
Yashraj S. Kulkarni ◽  
Tina L. Amyes ◽  
John Richard ◽  
Shina Caroline Lynn Kamerlin
Keyword(s):  
Active Site ◽  
Triosephosphate Isomerase ◽  
Valence Bond ◽  
Side Chains ◽  
Wild Type ◽  
Empirical Valence Bond

Manuscript and supporting information outlining an analysis of an extended Brønsted relationship obtained from empirical valence bond simulations of substrate deprotonation catalyzed by wild-type and mutant variants of triosephosphate isomerase.

The Influence of the Aromatic Amino Acid Side-Chains on the Sign of the Soret Cotton Effect in Chironomus Hemoglobin (CTT III)

1972 ◽  
Vol 27 (5) ◽  
pp. 530-532 ◽  
Author(s):  
Jörg Fleischhauer ◽  
Axel Wollmer
Keyword(s):  
Amino Acid ◽  
Aromatic Amino Acid ◽  
Cotton Effect ◽  
Side Chain ◽  
Side Chains ◽  
Aromatic Side Chain ◽  
Rotational Strength ◽  
Amino Acid Side Chains ◽  
Atomic Coordinates

The origin of the positive Soret Cotton effect of myoglobin was calculated by Hsu and WOODY on the basis of a mechanism taking into account the coupling of the Soret and aromatic side-chain π—π* transitions. HUBER and coworkers have worked out the atomic coordinates of a monomeric insect hemoglobin which exhibits a negative Soret Cotton effect.It seemed of some importance to examine the capability of this mechanism to explain the observed inversion of sign. The calculations resulted indeed in a negative total rotational strength (—0,2 DBM), the main contributions arising from phenylalanine residues.

scholarly journals Effect of Side-Chain Variation on Single-Crystalline Structures for Revealing the Structure–Property Relationships of Organic Solar Cells

2020 ◽  
Vol 02 (01) ◽  
pp. 026-032
Author(s):  
Chen Yang ◽  
Liu Yuan ◽  
Ruimin Zhou ◽  
Zhen Wang ◽  
Jianqi Zhang ◽  
...  
Keyword(s):  
Solar Cells ◽  
Single Crystal ◽  
Crystal Structures ◽  
Organic Solar Cells ◽  
Short Circuit ◽  
Photovoltaic Performance ◽  
Side Chains ◽  
Single Crystal Structures ◽  
Stacking Structure ◽  
Molecular Stacking

The molecular stacking assembly in the active layer plays a significant role in the photovoltaic performance of organic solar cells (OSCs). Here, we report two new small molecular donors with different side chains, FBT-O and FBT-H, and their corresponding fullerene-based OSCs. A slight change in the side chains led to a big difference in the power conversion efficiencies (PCEs). Although the molecular structures of the two donors are similar to each other, PCEs of the devices based on FBT-O were almost three times higher than those of the devices based on FBT-H, with manifold short-circuit current density, fill factor, as well as three orders of magnitude enhancement in the hole mobility. The difference in their single crystal structures was thoroughly investigated, whereby the FBT-O exhibited better planarity leading to appropriate phase separation and domain size. Furthermore, two-dimensional grazing-incidence wide-angle X-ray scattering results of the blend films revealed that the two donors retained a similar stacking structure as compared to the single-crystal structures, thus, establishing a clear relationship between the molecular stacking structure and the device performance.

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