scholarly journals Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Nandita Bodra ◽  
David Young ◽  
Leonardo Astolfi Rosado ◽  
Anna Pallo ◽  
Khadija Wahni ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Active Site ◽  
Glutathione Transferase ◽  
Normal Mode Analysis ◽  
Conformational Flexibility ◽  
Dehydroascorbate Reductase ◽  
Mode Analysis ◽  
Direct Role ◽  
Active Site Motif ◽  
Catalytic Cysteine

Abstract Dehydroascorbate reductase (DHAR) catalyzes the glutathione (GSH)-dependent reduction of dehydroascorbate and plays a direct role in regenerating ascorbic acid, an essential plant antioxidant vital for defense against oxidative stress. DHAR enzymes bear close structural homology to the glutathione transferase (GST) superfamily of enzymes and contain the same active site motif, but most GSTs do not exhibit DHAR activity. The presence of a cysteine at the active site is essential for the catalytic functioning of DHAR, as mutation of this cysteine abolishes the activity. Here we present the crystal structure of DHAR2 from Arabidopsis thaliana with GSH bound to the catalytic cysteine. This structure reveals localized conformational differences around the active site which distinguishes the GSH-bound DHAR2 structure from that of DHAR1. We also unraveled the enzymatic step in which DHAR releases oxidized glutathione (GSSG). To consolidate our structural and kinetic findings, we investigated potential conformational flexibility in DHAR2 by normal mode analysis and found that subdomain mobility could be linked to GSH binding or GSSG release.

scholarly journals Structure and dynamics of a cold-active esterase reveals water entropy and active site accessibility as the likely drivers for cold-adaptation

2021 ◽  
Author(s):  
Nehad Noby ◽  
Husam Sabah Auhim ◽  
Rachel L. Johnson ◽  
Harley Worthy ◽  
Amira M. Embaby ◽  
...  
Keyword(s):  
Active Site ◽  
Cold Adaptation ◽  
Normal Mode Analysis ◽  
Hydrophobic Effect ◽  
Mode Analysis ◽  
Water Solvent ◽  
Rigidity Analysis ◽  
Helical Content ◽  
Cold Active ◽  
Cold Adaption

AbstractCold-active esterases hold great potential for undertaking useful biotransformations at low temperatures. Here, we determined the structure of a cold active family IV esterase (EstN7) cloned from Bacillus cohnii strain N1, which has an apparent melting temperature of 26°C. EstN7 is a dimer with a classical α/β hydrolase fold. It has an acidic surface that is thought to play a role in cold-adaption by retaining solvation under changed water solvent entropy at lower temperatures. However, dynamics do not appear to play a major role in cold adaption. Comparison of B-factors with the closest related mesophilic and thermophilic esterases suggests there is little difference in dynamics with the catalytically important N-terminal cap comprising the main dynamic element. Molecular dynamics, rigidity analysis, normal mode analysis and geometric simulations of motion confirm the flexibility of the cap region but suggest that the rest of the protein is largely rigid. Rigidity analysis indicates the distribution of hydrophobic tethers is appropriate to colder conditions, where the hydrophobic effect is weaker than in mesophilic conditions due to reduced water entropy. The conformation of the cap region is significantly different to EstN7’s closest relatives, forming a bridge-like structure with reduced helical content providing more than one access tunnel through to the active site. Thus, it is likely that increased substrate accessibility and tolerance to changes in water entropy are the main drivers of EstN7’s cold adaptation rather than changes in dynamics.

scholarly journals Structural Insights into the Allosteric site of Arabidopsis NADP-Malic Enzyme 2: Role of the Second Sphere Residues in the Regulatory Signal Transmission

2021 ◽  
Author(s):  
Mariel Claudia Gerrard Wheeler ◽  
Cintia Lucía Arias ◽  
Juliana Juliana da Fonseca Rezende e Mello ◽  
Nuria Cirauqui Diaz ◽  
Carlos Rangel Rodrigues ◽  
...  
Keyword(s):  
Normal Mode ◽  
Conformational Changes ◽  
Active Site ◽  
Normal Mode Analysis ◽  
Signal Transmission ◽  
Allosteric Regulation ◽  
3D Structure ◽  
Mode Analysis ◽  
Allosteric Site ◽  
Structural Determinants

Abstract Structure-function studies contribute to deciphering how small modifications in the primary structure could introduce desirable characteristics into enzymes without affecting its overall functioning. Malic enzymes (ME) are ubiquitous and responsible for a wide variety of functions. The availability of a high number of ME crystal structures from different species facilitates comparisons between sequence and structure. Specifically, the structural determinants necessary for fumarate allosteric regulation of ME has been of particular interest. NADP-ME2 from Arabidopsis thaliana exhibits a distinctive and complex regulation by fumarate, acting as an activator or an inhibitor according to substrate and effector concentrations. However, the 3D structure for this enzyme is not yet reported. In this work, we characterized the NADP-ME2 allosteric site by structural modeling, molecular docking, normal mode analysis and mutagenesis. The regulatory site model and its docking analysis suggested that other C4 acids including malate, NADP-ME2 substrate, could also fit into fumarate’s pocket. Besides, a non-conserved cluster of hydrophobic residues in the second sphere of the allosteric site was identified. The substitution of one of those residues, L62, by a less flexible residue as tryptophan, resulted in a complete loss of fumarate activation and a reduction of substrate affinities for the active site. In addition, normal mode analysis indicated that conformational changes leading to the activation could originate in the region surrounding L62, extending through the allosteric site till the active site. Finally, the results in this work contribute to the understanding of structural determinants necessary for allosteric regulation providing new insights for enzyme optimization.

scholarly journals Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome

2021 ◽  
Author(s):  
Miquel Huix-Rotllant ◽  
Karno Schwinn ◽  
Nicolas Ferré
Keyword(s):  
Arabidopsis Thaliana ◽  
Infrared Spectroscopy ◽  
Ir Spectra ◽  
Normal Mode ◽  
Infrared Spectra ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Biological Macromolecules ◽  
Electrostatic Embedding

Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.

scholarly journals Erratum: Arabidopsis thaliana dehydroascorbate reductase 2: Conformational flexibility during catalysis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Nandita Bodra ◽  
David Young ◽  
Leonardo Astolfi Rosado ◽  
Anna Pallo ◽  
Khadija Wahni ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Conformational Flexibility ◽  
Dehydroascorbate Reductase

Application of the ESMACS Binding Free Energy Protocol to a Highly Varied Ligand Dataset: Lactate Dehydogenase A

2019 ◽  
Author(s):  
David Wright ◽  
Fouad Husseini ◽  
Shunzhou Wan ◽  
Christophe Meyer ◽  
Herman Van Vlijmen ◽  
...  
Keyword(s):  
Free Energy ◽  
Surface Area ◽  
Binding Free Energy ◽  
Normal Mode Analysis ◽  
Binding Mode ◽  
Accessible Surface Area ◽  
Solvent Accessible Surface Area ◽  
Mode Analysis ◽  
Energy Calculation ◽  
Accessible Surface

<div>Here, we evaluate the performance of our range of ensemble simulation based binding free energy calculation protocols, called ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) for use in fragment based drug design scenarios. ESMACS is designed to generate reproducible binding affinity predictions from the widely used molecular mechanics Poisson-Boltzmann surface area (MMPBSA) approach. We study ligands designed to target two binding pockets in the lactate dehydogenase A target protein, which vary in size, charge and binding mode. When comparing to experimental results, we obtain excellent statistical rankings across this highly diverse set of ligands. In addition, we investigate three approaches to account for entropic contributions not captured by standard MMPBSA calculations: (1) normal mode analysis, (2) weighted solvent accessible surface area (WSAS) and (3) variational entropy. </div>

RAMAN SPECTRA OF TITANIUM DI-, TRI-, AND TETRA-CHLORIDES

2001 ◽  
Vol 15 (28n30) ◽  
pp. 3865-3868 ◽  
Author(s):  
H. MIYAOKA ◽  
T. KUZE ◽  
H. SANO ◽  
H. MORI ◽  
G. MIZUTANI ◽  
...  
Keyword(s):  
Force Constant ◽  
Raman Spectra ◽  
Normal Mode ◽  
Raman Band ◽  
Normal Mode Analysis ◽  
Force Constants ◽  
Mode Analysis ◽  
Oxidation Number

We have obtained the Raman spectra of TiCl n (n= 2, 3, and 4). Assignments of the observed Raman bands were made by a normal mode analysis. The force constants were determined from the observed Raman band frequencies. We have found that the Ti-Cl stretching force constant increases as the oxidation number of the Ti species increases.

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