scholarly journals Gas Sensing by Bacterial H-NOX Proteins: An MD Study

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2882 ◽  
Author(s):  
Ahmed M. Rozza ◽  
Dóra K. Menyhárd ◽  
Julianna Oláh
Keyword(s):  
Gas Sensing ◽  
Hydrophobic Interactions ◽  
Transport Systems ◽  
Alternative Mode ◽  
Channel System ◽  
Gas Molecule ◽  
O2 Diffusion ◽  
Dynamics Simulations ◽  
And Storage ◽  
Kinetics Of

Gas sensing is crucial for both prokaryotes and eukaryotes and is primarily performed by heme-based sensors, including H-NOX domains. These systems may provide a new, alternative mode for transporting gaseous molecules in higher organisms, but for the development of such systems, a detailed understanding of the ligand-binding properties is required. Here, we focused on ligand migration within the protein matrix: we performed molecular dynamics simulations on three bacterial (Ka, Ns and Cs) H-NOX proteins and studied the kinetics of CO, NO and O2 diffusion. We compared the response of the protein structure to the presence of ligands, diffusion rate constants, tunnel systems and storage pockets. We found that the rate constant for diffusion decreases in the O2 > NO > CO order in all proteins, and in the Ns > Ks > Cs order if single-gas is considered. Competition between gases seems to seriously influence the residential time of ligands spent in the distal pocket. The channel system is profoundly determined by the overall fold, but the sidechain pattern has a significant role in blocking certain channels by hydrophobic interactions between bulky groups, cation–π interactions or hydrogen bonding triads. The majority of storage pockets are determined by local sidechain composition, although certain functional cavities, such as the distal and proximal pockets are found in all systems. A major guideline for the design of gas transport systems is the need to chemically bind the gas molecule to the protein, possibly joining several proteins with several heme groups together.

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

scholarly journals Morphology, energetics and growth kinetics of diphenylalanine fibres

2021 ◽  
Author(s):  
Phillip Mark Rodger ◽  
Caroline Montgomery ◽  
Giovanni Costantini ◽  
Alison Rodger
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Growth Kinetics ◽  
Dynamics Simulations ◽  
Kinetics Of

The formation and stability of diphenylalanine fibres are studied by combining molecular dynamics simulations with microscopy and spectroscopy experiments, quantitatively detailing their morphology, energetics and growth kinetics.

Insights into the roles of charged residues in substrate binding and mode of action of mannuronan C-5 epimerase AlgE4

Glycobiology ◽  
2021 ◽  
Author(s):  
Margrethe Gaardløs ◽  
Sergey A Samsonov ◽  
Marit Sletmoen ◽  
Maya Hjørnevik ◽  
Gerd Inger Sætrom ◽  
...  
Keyword(s):  
Optical Tweezers ◽  
Conformational Changes ◽  
Molecular Mechanisms ◽  
Hydrophobic Interactions ◽  
Substrate Binding ◽  
Interdisciplinary Approach ◽  
Product Formation ◽  
Titration Calorimetry ◽  
Binding Groove ◽  
Dynamics Simulations

Abstract Mannuronan C-5 epimerases catalyse the epimerization of monomer residues in the polysaccharide alginate, changing the physical properties of the biopolymer. The enzymes are utilized to tailor alginate to numerous biological functions by alginate-producing organisms. The underlying molecular mechanisms that control the processive movement of the epimerase along the substrate chain is still elusive. To study this, we have used an interdisciplinary approach combining molecular dynamics simulations with experimental methods from mutant studies of AlgE4, where initial epimerase activity and product formation were addressed with NMR spectroscopy, and characteristics of enzyme-substrate interactions were obtained with isothermal titration calorimetry and optical tweezers. Positive charges lining the substrate-binding groove of AlgE4 appear to control the initial binding of poly-mannuronate, and binding also seems to be mediated by both electrostatic and hydrophobic interactions. After the catalytic reaction, negatively charged enzyme residues might facilitate dissociation of alginate from the positive residues, working like electrostatic switches, allowing the substrate to translocate in the binding groove. Molecular simulations show translocation increments of two monosaccharide units before the next productive binding event resulting in MG-block formation, with the epimerase moving with its N-terminus towards the reducing end of the alginate chain. Our results indicate that the charge pair R343-D345 might be directly involved in conformational changes of a loop that can be important for binding and dissociation. The computational and experimental approaches used in this study complement each other, allowing for a better understanding of individual residues’ roles in binding and movement along the alginate chains.

scholarly journals Stability Kinetics of Influenza Vaccine Coated onto Microneedles During Drying and Storage

2010 ◽  
Vol 28 (1) ◽  
pp. 135-144 ◽  
Author(s):  
Yeu-Chun Kim ◽  
Fu-Shi Quan ◽  
Richard W. Compans ◽  
Sang-Moo Kang ◽  
Mark R. Prausnitz
Keyword(s):  
Influenza Vaccine ◽  
Stability Kinetics ◽  
And Storage ◽  
Kinetics Of

scholarly journals Fibronectin–collagen binding and requirement during cellular adhesion

1980 ◽  
Vol 186 (2) ◽  
pp. 551-559 ◽  
Author(s):  
Leslie I. Gold ◽  
Edward Pearlstein
Keyword(s):  
Chick Embryo ◽  
Human Plasma ◽  
Hydrophobic Interactions ◽  
Human Fibroblasts ◽  
Sodium Dodecyl ◽  
Cellular Adhesion ◽  
Adhesion Assay ◽  
Human Umbilical Cord ◽  
Ionic Detergents ◽  
Kinetics Of

Fibronectin isolated from human plasma and from the extracellular matrices of cell monolayers mediates the attachment in vitro and spreading of trypsin-treated cells on a collagen substratum. Fibronectin-dependent kinetics of cellular attachment to collagen were studied for several adherent cell types. It was shown that trypsin-treated human umbilical-cord cells, mouse sarcoma CMT81 cells, endothelial cells, and human fibroblasts from a patient with Glanzmann's disease were completely dependent on fibronectin for their attachment to collagen, whereas guinea-pig and monkey smooth-muscle cells and chick-embryo secondary fibroblasts displayed varying degrees of dependence on fibronectin for their attachment. Radiolabelled human plasma fibronectin possessed similar affinity for collagen types I, II and III from a variety of sources. The fibronectin bound equally well to the collagens with or without prior urea treatment. However, in the fibronectin-mediated adhesion assay using PyBHK fibroblasts, a greater number of cells adhered and more spreading was observed on urea-treated collagen. Fibronectin extracted from the extracellular matrix of chick-embryo fibroblasts and that purified from human plasma demonstrated very similar kinetics of complexing to collagencoated tissue-culture dishes. Fibronectin from both sources bound to collagen in the presence of 0.05–4.0m-NaCl and over the pH range 2.6–10.6. The binding was inhibited when fibronectin was incubated with 40–80% ethylene glycol, the ionic detergents sodium dodecyl sulphate and deoxycholate, and the non-ionic detergents Nonidet P-40, Tween 80 and Triton X-100, all at a concentration of 0.1%. From these results we proposed that fibronectin–collagen complexing is mainly attributable to hydrophobic interactions.

Mechanisms and kinetics of initial pyrolysis and combustion reactions of 1,1-diamino-2,2-dinitroethylene from density functional tight-binding molecular dynamics simulations

2019 ◽  
Vol 97 (11) ◽  
pp. 795-804 ◽  
Author(s):  
Dong Xiang ◽  
Weihua Zhu
Keyword(s):  
Activation Energy ◽  
Molecular Dynamics ◽  
Density Functional ◽  
Tight Binding ◽  
Combustion Process ◽  
Exponential Factor ◽  
Three Stages ◽  
Dynamics Simulations ◽  
Combustion Processes ◽  
Kinetics Of

The density functional tight-binding molecular dynamics approach was used to study the mechanisms and kinetics of initial pyrolysis and combustion reactions of isolated and multi-molecular FOX-7. Based on the thermal cleavage of bridge bonds, the pyrolysis process of FOX-7 can be divided into three stages. However, the combustion process can be divided into five decomposition stages, which is much more complex than the pyrolysis reactions. The vibrations in the mean temperature contain nodes signifying the formation of new products and thereby the transitions between the various stages in the pyrolysis and combustion processes. Activation energy and pre-exponential factor for the pyrolysis and combustion reactions of FOX-7 were obtained from the kinetic analysis. It is found that the activation energy of its pyrolysis and combustion reactions are very low, making both take place fast. Our simulations provide the first atomic-level look at the full dynamics of the complicated pyrolysis and combustion process of FOX-7.

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