Exploration of CH⋯π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling

TMADH (trimethylamine dehydrogenase) is a complex iron-sulphur flavoprotein that forms a soluble electron-transfer complex with ETF (electron-transferring flavoprotein). The mechanism of electron transfer between TMADH and ETF has been studied using stopped-flow kinetic and mutagenesis methods, and more recently by X-ray crystallography. Potentiometric methods have also been used to identify key residues involved in the stabilization of the flavin radical semiquinone species in ETF. These studies have demonstrated a key role for 'conformational sampling' in the electron-transfer complex, facilitated by two-site contact of ETF with TMADH. Exploration of three-dimensional space in the complex allows the FAD of ETF to find conformations compatible with enhanced electronic coupling with the 4Fe-4S centre of TMADH. This mechanism of electron transfer provides for a more robust and accessible design principle for interprotein electron transfer compared with simpler models that invoke the collision of redox partners followed by electron transfer. The structure of the TMADH-ETF complex confirms the role of key residues in electron transfer and molecular assembly, originally suggested from detailed kinetic studies in wild-type and mutant complexes, and from molecular modelling.

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Intrinsic Stacking Interactions of Natural and Artificial Nucleobases

10.26434/chemrxiv.11400405 ◽

2019 ◽

Author(s):

Drew P. Harding ◽

Laura J. Kingsley ◽

Glen Spraggon ◽

Steven Wheeler

Keyword(s):

Gas Phase ◽

Electrostatic Interactions ◽

Density Functional ◽

Molecular Descriptors ◽

Stacking Interactions ◽

Interaction Energies ◽

Functional Theory ◽

Binding Partner ◽

Heavy Atoms ◽

Wide Range

The intrinsic (gas-phase) stacking energies of natural and artificial nucleobases were explored using density functional theory (DFT) and correlated ab initio methods. Ranking the stacking strength of natural nucleobase dimers revealed a preference in binding partner similar to that seen from experiments, namely G > C > A > T > U. Decomposition of these interaction energies using symmetry-adapted perturbation theory (SAPT) showed that these dispersion dominated interactions are modulated by electrostatics. Artificial nucleobases showed a similar stacking preference for natural nucleobases and were also modulated by electrostatic interactions. A robust predictive multivariate model was developed that quantitively predicts the maximum stacking interaction between natural and a wide range of artificial nucleobases using molecular descriptors based on computed electrostatic potentials (ESPs) and the number of heavy atoms. This model should find utility in designing artificial nucleobase analogs that exhibit stacking interactions comparable to those of natural nucleobases. Further analysis of the descriptors in this model unveil the origin of superior stacking abilities of certain nucleobases, including cytosine and guanine.

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The intermolecular anthracene-transfer in a regiospecific antipodal C60 difunctionalization

10.26434/chemrxiv.11968743.v2 ◽

2020 ◽

Author(s):

Radu Talmazan ◽

Klaus R. Liedl ◽

Bernhard Kräutler ◽

Maren Podewitz

Keyword(s):

Noncovalent Interactions ◽

Interaction Model ◽

Alder Reaction ◽

Diels Alder ◽

Stacking Interactions ◽

Pi Stacking ◽

Diels Alder Reaction ◽

Double Decker ◽

Anthracene Molecule ◽

New Strategies

We analyze the mechanism of the topochemically controlled difunctionalization of C60 and anthracene, where an anthracene molecule is transferred from one C60 monoadduct to another one under exclusive formation of equal amounts of C60 and the difficult to make antipodal C60 bisadduct. Our herein disclosed dispersion corrected DFT studies show the anthracene transfer to take place in a synchronous retro Diels-Alder/Diels-Alder reaction: an anthracene molecule dissociates from one fullerene under formation of an intermediate, while already undergoing stabilizing interactions with both neighboring fullerenes, facilitating the reaction kinetically. In the intermediate, a planar anthracene molecule is sandwiched between two neighboring fullerenes and forms equally strong "double-decker" type pi-pi stacking interactions with both of these fullerenes. Analysis with the distorsion interaction model shows that the anthracene unit of the intermediate is almost planar with minimal distorsions. This analysis sheds light on the existence of noncovalent interactions engaging both faces of a planar polyunsaturated ring and two convex fullerene surfaces in an unprecedented 'inverted sandwich' structure. Hence, it sheds light on new strategies to design functional fullerene based materials.

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A Chemical Perspective to the Anti-Amyloid Action of Compounds and a Nanoparticle Based Assay for Screening Amyloid Inhibitors

10.26434/chemrxiv.7819661 ◽

2020 ◽

Author(s):

Nidhi Gour ◽

Bharti Koshti

Keyword(s):

Memory Loss ◽

Cost Effective ◽

Structural Motif ◽

Rapid Screening ◽

Stacking Interactions ◽

Aromatic Rings ◽

Amyloid Fibers ◽

Aromatic Stacking ◽

Cost Effective Technique ◽

The Brain

Aggregation of amyloid beeta 1-42 (Aβ42) peptide causes the formation of clustered deposits knows as amyloid plaques in the brain which leads to neuronal dysfunction and memory loss and associated with many neurological disorders including Alzheimer’s and Parkinson’s. Aβ42 has core structural motif with phenylalanine at the 19 and 20 positions. The diphenylalanine (FF) residue plays a crucial role in the formation of amyloid fibers and serves as model peptide for studying Aβ42 aggregation. FF self-assembles to well-ordered tubular morphology via aromatic pi-pi stackings. Our studies, suggest that the aromatic rings present in the anti-amyloidogenic compounds may interact with the pi-pi stacking interactions present in the FF. Even the compounds which do not have aromatic rings, like cyclodextrin and cucurbituril show anti-amyloid property due to the binding of aromatic ring inside the guest cavity. Hence, our studies also suggest that compounds which may have a functional moiety capable of interacting with the aromatic stacking interactions might be tested for their anti-amyloidogenic properties. Further, in this manuscript, we have proposed two novel nanoparticle based assays for the rapid screening of amyloid inhibitors. In the first assay, interaction between biotin-tagged FF peptide and the streptavidin labelled gold nanoparticles (s-AuNPs) were used. In another assay, thiol-Au interactions were used to develop an assay for detection of amyloid inhibitors. It is envisaged that the proposed analytical method will provide a simple, facile and cost effective technique for the screening of amyloid inhibitors and may be of immense practical implications to find the therapeutic remedies for the diseases associated with the protein aggregation.

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Predicting the Strength of Stacking Interactions Between Heterocycles and Aromatic Amino Acid Side Chains

10.26434/chemrxiv.7628939.v2 ◽

2019 ◽

Author(s):

Andrea N. Bootsma ◽

Analise C. Doney ◽

Steven Wheeler

Keyword(s):

Amino Acid ◽

Binding Sites ◽

Aromatic Amino Acid ◽

Aromatic Amino Acids ◽

Biologically Active ◽

Side Chains ◽

Stacking Interactions ◽

Inhibitor Binding ◽

Protein Binding Sites ◽

Amino Acid Side Chains

Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. Based on rigorous ab initio data, we have devised a simple predictive model of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. This model provides rapid predictions of the stacking ability of a given heterocycle based on readily-computed heterocycle descriptors. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow simple predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual model for understanding stacking interactions in protein binding sites and optimizing inhibitor binding in drug design.

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Self-Recognizing π-π Stacking Interactions Designed for the Generation of Ultrastable Mesoporous Hydrogen-Bonded Organic Frameworks

10.26434/chemrxiv.9729494 ◽

2019 ◽

Author(s):

KAIKAI MA ◽

Peng Li ◽

John Xin ◽

Yongwei Chen ◽

Zhijie Chen ◽

...

Keyword(s):

Pore Size ◽

Fiber Composite ◽

Aqueous Media ◽

Stacking Interactions ◽

Mustard Gas ◽

X Ray Diffraction ◽

X Ray ◽

Expansion Strategy ◽

Π Stacking ◽

Hydrogen Bonded

Creating crystalline porous materials with large pores is typically challenging due to undesired interpen-etration, staggered stacking, or weakened framework stability. Here, we report a pore size expansion strategy by self-recognizing π-π stacking interactions in a series of two-dimensional (2D) hydrogen–bonded organic frameworks (HOFs), HOF-10x (x=0,1,2), self-assembled from pyrene-based tectons with systematic elongation of π-conjugated molecular arms. This strategy successfully avoids interpene-tration or staggered stacking and expands the pore size of HOF materials to access mesoporous HOF-102, which features a surface area of ~ 2,500 m2/g and the largest pore volume (1.3 cm3/g) to date among all reported HOFs. More importantly, HOF-102 shows significantly enhanced thermal and chemical stability as evidenced by powder x-ray diffraction and N2 isotherms after treatments in chal-lenging conditions. Such stability enables the adsorption of dyes and cytochrome c from aqueous media by HOF-102 and affords a processible HOF-102/fiber composite for the efficient photochemical detox-ification of a mustard gas simulant.

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FSATOOL: A useful tool to do the conformational sampling and trajectory analysis work for biomolecules

Journal of Computational Chemistry ◽

10.1002/jcc.26083 ◽

2019 ◽

Vol 41 (2) ◽

pp. 156-164

Author(s):

Haomiao Zhang ◽

Qiankun Gong ◽

Haozhe Zhang ◽

Changjun Chen

Keyword(s):

Trajectory Analysis ◽

Conformational Sampling

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On the Use of the Discrete Constant pH Molecular Dynamics to Describe the Conformational Space of Peptides

Polymers ◽

10.3390/polym13010099 ◽

2020 ◽

Vol 13 (1) ◽

pp. 99

Author(s):

Cristian Privat ◽

Sergio Madurga ◽

Francesc Mas ◽

Jaime Rubio-Martínez

Keyword(s):

Molecular Dynamics ◽

Amino Acids ◽

Md Simulations ◽

Point Of View ◽

Conformational Space ◽

Conformational Sampling ◽

Protonation State ◽

Constant Ph ◽

Biochemical Systems ◽

Constant Ph Molecular Dynamics

Solvent pH is an important property that defines the protonation state of the amino acids and, therefore, modulates the interactions and the conformational space of the biochemical systems. Generally, this thermodynamic variable is poorly considered in Molecular Dynamics (MD) simulations. Fortunately, this lack has been overcome by means of the Constant pH Molecular Dynamics (CPHMD) methods in the recent decades. Several studies have reported promising results from these approaches that include pH in simulations but focus on the prediction of the effective pKa of the amino acids. In this work, we want to shed some light on the CPHMD method and its implementation in the AMBER suitcase from a conformational point of view. To achieve this goal, we performed CPHMD and conventional MD (CMD) simulations of six protonatable amino acids in a blocked tripeptide structure to compare the conformational sampling and energy distributions of both methods. The results reveal strengths and weaknesses of the CPHMD method in the implementation of AMBER18 version. The change of the protonation state according to the chemical environment is presumably an improvement in the accuracy of the simulations. However, the simulations of the deprotonated forms are not consistent, which is related to an inaccurate assignment of the partial charges of the backbone atoms in the CPHMD residues. Therefore, we recommend the CPHMD methods of AMBER program but pointing out the need to compare structural properties with experimental data to bring reliability to the conformational sampling of the simulations.

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Examination of Aggregation Induced Enhanced Emission in a Propeller Shaped Chiral- Nonconjugated Blue Emitter from Restricted Intramolecular Rotation and J Type π⋯π Stacking Interactions

Physical Chemistry Chemical Physics ◽

10.1039/d0cp06690g ◽

2021 ◽

Author(s):

Gul Yakali

Keyword(s):

Thin Film ◽

Small Molecules ◽

Solid Phase ◽

Stacking Interactions ◽

Optoelectronic Materials ◽

Π Stacking ◽

Intramolecular Rotation

Fluorescent organic small molecules with the property of aggregation induced enhanced emission in the solid phase (crystall or thin film) have great attention for the design of optoelectronic materials. Generally,...

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