scholarly journals Computational Investigation of O2 Diffusion Through an Intra–molecular Tunnel in AlkB; Influence of Polarization on O2 Transport

2017 ◽  
Author(s):  
Hedieh Torabifard ◽  
G. Andrés Cisneros
Keyword(s):  
Active Site ◽  
Oxidation Mechanism ◽  
Md Simulations ◽  
Potential Of Mean Force ◽  
E Coli ◽  
O2 Diffusion ◽  
Molecular Tunnels ◽  
Migration Pathways ◽  
Conserved Residue ◽  
Initial Crystal

AbstractE. Coli AlkB catalyzes the direct dealkylation of various alkylated bases in damaged DNA. The diffusion of molecular Oxygen to the active site in AlkB is an essential step for the oxidative dealkylation activity. Despite detailed studies on the stepwise oxidation mechanism of AlkB, there is no conclusive picture of how O2 molecules reach the active site of the protein. Yu et al. (Nature,439, 879) proposed the existence of an intra–molecular tunnel based on their initial crystal structures of AlkB. We have employed computational simulations to investigate possible migration pathways inside AlkB for O2 molecules. Extensive molecular dynamics (MD) simulations, including explicit ligand sampling and potential of mean force (PMF) calculations, have been performed to provide a microscopic description of the O2 delivery pathway in AlkB. Analysis of intra–molecular tunnels using the CAVER software indicates two possible pathways for O2 to diffuse into the AlkB active site. Explicit ligand sampling simulations suggests that only one of these tunnels provides a viable route. The free energy path for an oxygen molecule to travel along each of these tunnels has been determined with AMBER and AMOEBA. Both PMFs indicate passive transport of O2 from the surface of the protein. However, the inclusion of explicit polarization shows a very large barrier for diffusion of the co–substrate out of the active site, compared with the non–polarizable potential. In addition, our results suggest that the mutation of a conserved residue along the tunnel, Y178, has dramatic effects on the dynamics of AlkB and on the transport of O2 along the tunnel.

Effects of viscosity and osmotic stress on the reaction of human butyrylcholinesterase with cresyl saligenin phosphate, a toxicant related to aerotoxic syndrome: kinetic and molecular dynamics studies

2013 ◽  
Vol 454 (3) ◽  
pp. 387-399 ◽  
Author(s):  
Patrick Masson ◽  
Sofya Lushchekina ◽  
Lawrence M. Schopfer ◽  
Oksana Lockridge
Keyword(s):  
Osmotic Stress ◽  
Osmotic Pressure ◽  
Active Site ◽  
Md Simulations ◽  
Catalytic Triad ◽  
Wild Type ◽  
Irreversible Inhibitor ◽  
Enzyme Active Site ◽  
Diffusion Controlled ◽  
Peripheral Site

CSP (cresyl saligenin phosphate) is an irreversible inhibitor of human BChE (butyrylcholinesterase) that has been involved in the aerotoxic syndrome. Inhibition under pseudo-first-order conditions is biphasic, reflecting a slow equilibrium between two enzyme states E and E′. The elementary constants for CSP inhibition of wild-type BChE and D70G mutant were determined by studying the dependence of inhibition kinetics on viscosity and osmotic pressure. Glycerol and sucrose were used as viscosogens. Phosphorylation by CSP is sensitive to viscosity and is thus strongly diffusion-controlled (kon≈108 M−1·min−1). Bimolecular rate constants (ki) are about equal to kon values, making CSP one of the fastest inhibitors of BChE. Sucrose caused osmotic stress because it is excluded from the active-site gorge. This depleted the active-site gorge of water. Osmotic activation volumes, determined from the dependence of ki on osmotic pressure, showed that water in the gorge of the D70G mutant is more easily depleted than that in wild-type BChE. This demonstrates the importance of the peripheral site residue Asp70 in controlling the active-site gorge hydration. MD simulations provided new evidence for differences in the motion of water within the gorge of wild-type and D70G enzymes. The effect of viscosogens/osmolytes provided information on the slow equilibrium E⇌E′, indicating that alteration in hydration of a key catalytic residue shifts the equilibrium towards E′. MD simulations showed that glycerol molecules that substitute for water molecules in the enzyme active-site gorge induce a conformational change in the catalytic triad residue His438, leading to the less reactive form E′.

scholarly journals The structure of the metallo-β-lactamase VIM-2 in complex with a triazolylthioacetamide inhibitor

2016 ◽  
Vol 72 (11) ◽  
pp. 813-819 ◽  
Author(s):  
Tony Christopeit ◽  
Ke-Wu Yang ◽  
Shao-Kang Yang ◽  
Hanna-Kirsti S. Leiros
Keyword(s):  
Public Health ◽  
Crystal Structure ◽  
Active Site ◽  
Drug Target ◽  
Zinc Ions ◽  
Clinical Use ◽  
Global Public Health ◽  
Promising Strategy ◽  
Conserved Residue ◽  
Substrate Spectrum

The increasing number of pathogens expressing metallo-β-lactamases (MBLs), and in this way achieving resistance to β-lactam antibiotics, is a significant threat to global public health. A promising strategy to treat such resistant pathogens is the co-administration of MBL inhibitors together with β-lactam antibiotics. However, an MBL inhibitor suitable for clinical use has not yet been identified. Verona integron-encoded metallo-β-lactamase 2 (VIM-2) is a widespread MBL with a broad substrate spectrum and hence is an interesting drug target for the treatment of β-lactam-resistant infections. In this study, three triazolylthioacetamides were tested as inhibitors of VIM-2. One of the tested compounds showed clear inhibition of VIM-2, with an IC50of 20 µM. The crystal structure of the inhibitor in complex with VIM-2 was obtained by DMSO-free co-crystallization and was solved at a resolution of 1.50 Å. To our knowledge, this is the first structure of a triazolylthioacetamide inhibitor in complex with an MBL. Analysis of the structure shows that the inhibitor binds to the two zinc ions in the active site of VIM-2 and revealed detailed information on the interactions involved. Furthermore, the crystal structure showed that binding of the inhibitor induced a conformational change of the conserved residue Trp87.

Diffusion of atomic oxygen relevant to water formation in amorphous interstellar ices

2014 ◽  
Vol 168 ◽  
pp. 205-222 ◽  
Author(s):  
Myung Won Lee ◽  
Markus Meuwly
Keyword(s):  
Electrostatic Interactions ◽  
Atomic Oxygen ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Chemical Mechanism ◽  
Amorphous Ice ◽  
Migration Barriers ◽  
Water Formation ◽  
Interstellar Ices ◽  
Migration Pathways

Molecular dynamics (MD) simulations together with accurate physics-based force fields are employed to determine the mobility of atomic oxygen in amorphous ice at low temperatures, characteristic for conditions in interstellar ices. From the simulations it is found that the mobility of atomic oxygen ranges from 60 to 480 Å2 ns−1 in amorphous ice at temperatures between 50 and 200 K. Hence, the simulations establish that atomic oxygen is mobile to a certain degree and a chemical mechanism for water formation involving oxygen mobility is a realistic scenario. This is also confirmed by the computed migration barriers for oxygen diffusion by multiple umbrella sampling simulations, which yield barriers for diffusion in the range of 0.7–1.9 kcal mol−1. The physics-based force field – based on a multipolar expansion of the electrostatic interactions – yields more pronounced energetics for oxygen migration pathways compared to the conventional point-charge models employed in typical simulations. Once formed, the computed solvation free energy suggests that atomic oxygen thermodynamically prefers to be localized inside amorphous ice and is available for chemical reaction, which may be relevant to water formation in and on grains.

AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS

2007 ◽  
Vol 17 (02) ◽  
pp. 225-237 ◽  
Author(s):  
ALEXEI BYKHOVSKI ◽  
TATIANA GLOBUS ◽  
TATYANA KHROMOVA ◽  
BORIS GELMONT ◽  
DWIGHT WOOLARD
Keyword(s):  
Molecular Structure ◽  
Structural Similarity ◽  
Md Simulations ◽  
Detection Capability ◽  
Dna Structures ◽  
E Coli ◽  
Cellular Components ◽  
First Time ◽  
Insight Into ◽  
Specific Contribution

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

“Active Site” Dynamics: A Comparison of the Wild Type and Single Tryptophan Variants of E. Coli Thioredoxin

1993 ◽  
pp. 595-603
Author(s):  
Marvin D. Kemple ◽  
Kenneth E. Nollet ◽  
Peng Yuan ◽  
Franklyn G. Prendergast
Keyword(s):  
Active Site ◽  
Wild Type ◽  
E Coli

scholarly journals Defect structure in δ-Bi5PbY2O11.5

RSC Advances ◽  
2019 ◽  
Vol 9 (17) ◽  
pp. 9640-9653 ◽  
Author(s):  
Anna Borowska-Centkowska ◽  
Xi Liu ◽  
Marcin Krynski ◽  
Marzena Leszczynska ◽  
Wojciech Wrobel ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Ab Initio ◽  
Defect Structure ◽  
Md Simulations ◽  
Total Neutron ◽  
Vacancy Ordering ◽  
And Migration ◽  
Migration Pathways ◽  
Oxide Ion

Total neutron scattering analysis and ab initio MD simulations reveal details of oxide ion vacancy ordering and migration pathways.

scholarly journals Crystal Structures of E. coli Native MenH and Two Active Site Mutants

PLoS ONE ◽  
2013 ◽  
Vol 8 (4) ◽  
pp. e61325 ◽  
Author(s):  
Jodie M. Johnston ◽  
Ming Jiang ◽  
Zhihong Guo ◽  
Edward N. Baker
Keyword(s):  
Crystal Structures ◽  
Active Site ◽  
E Coli ◽  
Active Site Mutants

scholarly journals Hup-Type Hydrogenases of Purple Bacteria: Homology Modeling and Computational Assessment of Biotechnological Potential

2020 ◽  
Vol 21 (1) ◽  
pp. 366 ◽  
Author(s):  
Azat Vadimovich Abdullatypov
Keyword(s):  
Hydrophobic Interactions ◽  
Purple Bacteria ◽  
Three Dimensional ◽  
Small Subunit ◽  
Protein Docking ◽  
Intramolecular Interactions ◽  
Oligomeric State ◽  
E Coli ◽  
Membrane Bound ◽  
Molecular Tunnels

Three-dimensional structures of six closely related hydrogenases from purple bacteria were modeled by combining the template-based and ab initio modeling approach. The results led to the conclusion that there should be a 4Fe3S cluster in the structure of these enzymes. Thus, these hydrogenases could draw interest for exploring their oxygen tolerance and practical applicability in hydrogen fuel cells. Analysis of the 4Fe3S cluster’s microenvironment showed intragroup heterogeneity. A possible function of the C-terminal part of the small subunit in membrane binding is discussed. Comparison of the built models with existing hydrogenases of the same subgroup (membrane-bound oxygen-tolerant hydrogenases) was carried out. Analysis of intramolecular interactions in the large subunits showed statistically reliable differences in the number of hydrophobic interactions and ionic interactions. Molecular tunnels were mapped in the models and compared with structures from the PDB. Protein–protein docking showed that these enzymes could exchange electrons in an oligomeric state, which is important for oxygen-tolerant hydrogenases. Molecular docking with model electrode compounds showed mostly the same results as with hydrogenases from E. coli, H. marinus, R. eutropha, and S. enterica; some interesting results were shown in case of HupSL from Rba. sphaeroides and Rvi. gelatinosus.

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