Conformational Distortion Research Articles

Structural and dynamic effects of paraoxon binding to human acetylcholinesterase by X-ray crystallography and inelastic neutron scattering

Organophosphorus (OP) compounds, including nerve agents and some pesticides, covalently bind to the catalytic serine of human acetylcholinesterase (hAChE), thereby inhibiting acetylcholine hydrolysis necessary for efficient neurotransmission. Oxime antidotes can reactivate the OP-conjugated hAChE, but reactivation efficiency can be low for pesticides, such as paraoxon (POX). Understanding structural and dynamic determinants of OP inhibition and reactivation can provide insights to design improved reactivators. Here, X-ray structures of hAChE with unaged POX, with POX and oximes MMB4 and RS170B, and with MMB4 are reported. A significant conformational distortion of the acyl loop was observed upon POX binding, being partially restored to the native conformation by oximes. Neutron vibrational spectroscopy combined with molecular dynamics simulations showed that picosecond vibrational dynamics of the acyl loop soften in the ∼20-50cm-1 frequency range. The acyl loop structural perturbations may be correlated with its picosecond vibrational dynamics to yield more comprehensive template for structure-based reactivator design.

Volumetric parameterization with truncated hierarchical B-splines for isogeometric analysis

Constructing spline parameterizations for computational domains is one of the fundamental problems in isogeometric analysis. In this paper, we present an efficient method for parameterizing volumetric computational domains using truncated hierarchical B-splines (THB). To ensure the injectivity of the parameterization, we utilize a collocation-based framework where the foldovers are eliminated on an increasing collocation set until the injectivity can be verified. A local–global solver is employed to eliminate any foldover effectively by projecting the mapping onto a bounded conformal distortion space. Local refinement of THB splines is also performed to enlarge the injectivity space. Various sufficient conditions are proposed to check the injectivity of the mapping efficiently. The quality of the bijective mapping is further improved by optimizing a geometrical energy, which is also embedded in the collocation framework to ensure injectivity. A coarse-to-fine variant of our method, which is more robust, is also presented. THB splines not only reduce the number of degrees of freedom in the parametric representation, but also increase the possibility of producing a bijective parameterization by local refinement. Some examples are provided to demonstrate the efficiency, effectiveness and robustness of our method.

Novel Calcium-Binding Ablating Mutations Induce Constitutive RET Activity and Drive Tumorigenesis.

Comprehensive proteogenomic and in silico analyses of a vast number of VUSs identify a novel set of oncogenic and druggable mutations in the well-characterized RET oncogene.

Application of Computational Simulation Integrating Inhibition Kinetics for Detecting Tyrosinase Inhibitor: Salsalate Is a New Inhibitor.

Tyrosinase inhibitor developments have been widely attended by investigators for their various applications. A combination of virtual screening of docking simulations and biochemical inhibition kinetics was performed to find a new inhibitor of tyrosinase for the clinical application of an antipigment agent. We conducted docking simulations to detect tyrosinase key binding residues and used the detected binding residues to screen the NCBI PubChem database for probing tyrosinase binding compounds. The serial inhibition kinetics and spectrofluorimetry measurements were performed to validate the inhibitory effect on tyrosinase. We have detected 200 candidates and categorized them into four clusters. Among them, we successfully confirmed salsalate as a new inhibitor of tyrosinase measured by serial enzyme kinetics. Salsalate was detected as a reversible inhibitor of tyrosinase displaying a typical mixedtype inhibition manner (IC50 = 22.19 ± 1.01 mM; Ki = 19.98 ± 2.11 mM). Spectrofluorimetry measurement by integrating with 1-anilinonaphthalene-8-sulfonate showed that salsalate mainly induced a slight regional conformation distortion of the tyrosinase active site accompanied by a slight hydrophobic disruption. Our study suggests that salsalate is a potential anti-pigment drug via inhibition of tyrosinase activity and it might be applicable for dermatologic clinical application. Also, our study enlarges an insight into the salsalate drug application.

Constructing planar domain parameterization with HB-splines via quasi-conformal mapping

Constructing a high-quality parameterization of a computational domain is a fundamental research problem in isogeometric analysis, which has been extensively investigated so far. However, most of the current approaches employ non-uniform rational B-splines (NURBS) as the geometric representation of the physical domain. NURBS introduce redundant degrees of freedom due to their tensor-product structure. In this paper, we propose a new parameterization method for planar domains by adopting hierarchical B-splines (HB-splines) as the geometric representation that possess local refinement abilities. Starting from an initial parameterization such as a harmonic map, our method repeats the following two steps until a bijective parameterization with low distortion is achieved. First, a non-linear optimization model is proposed to compute a quasi-conformal map represented by HB-splines, and an efficient algorithm is provided to deal with this model by alternatively solving two quadratic optimization problems. Second, the parameterization is refined locally through HB-splines based on the bijectivity and conformal distortion of the parameterization. Several examples are demonstrated to verity the effectiveness and advantages of the proposed approach.

Intrinsic metrics under conformal and quasiregular mappings

The distortion of six different intrinsic metrics and quasi-metrics under conformal and quasiregular mappings is studied in a few simple domains $G\subsetneq\mathbb{R}^n$. The already known inequalities between the hyperbolic metric and these intrinsic metrics for points $x,y$ in the unit ball $\mathbb{B}^n$ are improved by limiting the absolute values of the points $x,y$ and the new results are then used to study the conformal distortion of the intrinsic metrics. For the triangular ratio metric between two points $x,y\in\mathbb{B}^n$, the conformal distortion is bounded in terms of the hyperbolic midpoint and the hyperbolic distance of $x,y$. Furthermore, quasiregular and quasiconformal mappings are studied, and new sharp versions of the Schwarz lemma are introduced.

Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics-Molecular Mechanics Framework.

A whole-exome capture and next-generation sequencing was applied to an 11 y/o patient with a clinical history of congenital hypotonia, generalized motor and cognitive neurodevelopmental delay, and severe cognitive deficit, and without any identifiable Syndromic pattern, and to her parents, we disclosed a de novo heterozygous pathogenic mutation, c.697_699del p.Phe233del (rs786204835)(ACMG classification PS2, PM1, PM2, PP5), harbored in the PURA gene (MIM*600473) (5q31.3), associated with Autosomal Dominant Mental Retardation 31 (MIM # 616158). We used the significant improvement in the accuracy of protein structure prediction recently implemented in AlphaFold that incorporates novel neural network architectures and training procedures based on the evolutionary, physical, and geometric constraints of protein structures. The wild-type (WT) sequence and the mutated sequence, missing the Phe233, were reconstructed. The predicted local Distance Difference Test (lDDT) for the PURAwt and the PURA–Phe233del showed that the occurrence of the Phe233del affects between 220–320 amino acids. The distortion in the PURA structural conformation in the ~5 Å surrounding area after the p.Phe233del produces a conspicuous disruption of the repeat III, where the DNA and RNA helix unwinding capability occurs. PURA Protein–DNA docking corroborated these results in an in silico analysis that showed a loss of the contact of the PURA–Phe233del III repeat domain model with the DNA. Together, (i) the energetic and stereochemical, (ii) the hydropathic indexes and polarity surfaces, and (iii) the hybrid Quantum Mechanics–Molecular Mechanics (QM–MM) analyses of the PURA molecular models demarcate, at the atomic resolution, the specific surrounding region affected by these mutations and pave the way for future cell-based functional analysis. To the best of our knowledge, this is the first report of a de novo mutation underpinning a PURA syndrome in a Latin American patient and highlights the importance of predicting the molecular effects in protein structure using artificial intelligence algorithms and molecular and atomic resolution stereochemical analyses.

Adaptive area-preserving parameterization of open and closed anatomical surfaces

The parameterization of open and closed anatomical surfaces is of fundamental importance in many biomedical applications. Spherical harmonics, a set of basis functions defined on the unit sphere, are widely used for anatomical shape description. However, establishing a one-to-one correspondence between the object surface and the entire unit sphere may induce a large geometric distortion in case the shape of the surface is too different from a perfect sphere. In this work, we propose adaptive area-preserving parameterization methods for simply-connected open and closed surfaces with the target of the parameterization being a spherical cap. Our methods optimize the shape of the parameter domain along with the mapping from the object surface to the parameter domain. The object surface will be globally mapped to an optimal spherical cap region of the unit sphere in an area-preserving manner while also exhibiting low conformal distortion. We further develop a set of spherical harmonics-like basis functions defined over the adaptive spherical cap domain, which we call the adaptive harmonics. Experimental results show that the proposed parameterization methods outperform the existing methods for both open and closed anatomical surfaces in terms of area and angle distortion. Surface description of the object surfaces can be effectively achieved using a novel combination of the adaptive parameterization and the adaptive harmonics. Our work provides a novel way of mapping anatomical surfaces with improved accuracy and greater flexibility. More broadly, the idea of using an adaptive parameter domain allows easy handling of a wide range of biomedical shapes.

Acrylamide fragment inhibitors that induce unprecedented conformational distortions in enterovirus 71 3C and SARS-CoV-2 main protease.

RNA viruses are critically dependent upon virally encoded proteases to cleave the viral polyproteins into functional proteins. Many of these proteases exhibit a similar fold and contain an essential catalytic cysteine, offering the opportunity to inhibit these enzymes with electrophilic small molecules. Here we describe the successful application of quantitative irreversible tethering (qIT) to identify acrylamide fragments that target the active site cysteine of the 3C protease (3Cpro) of Enterovirus 71, the causative agent of hand, foot and mouth disease in humans, altering the substrate binding region. Further, we re-purpose these hits towards the main protease (Mpro) of SARS-CoV-2 which shares the 3C-like fold and a similar active site. The hit fragments covalently link to the catalytic cysteine of Mpro to inhibit its activity. We demonstrate that targeting the active site cysteine of Mpro can have profound allosteric effects, distorting secondary structures to disrupt the active dimeric unit.

Organic Crystalline Optical Waveguides That Remain Elastic from −196 to ≈200 °C

AbstractOrganic crystals that are capable to deform (reversibly or irreversibly) similar to polymer materials have been widely reported over the past ten years. However, most of the reported organic crystals can only be elastically bent within a narrow temperature range, and reports on their thermal behavior that would encourage applications of these energy‐transducing elements in extreme conditions are not readily available. This work designs a linear and flat π‐conjugated molecule with double intramolecular hydrogen bonds that prevent thermally induced conformational distortions. The molecule assembles as a rigid building block into centimeter‐sized wide organic crystals that can be elastically bent over a temperature range spanning close to 400 °C, from −196 to ≈200 °C. The emission wavelength of the crystals is also temperature dependent, and can be continually tuned from 547 to 577 nm upon heating from 20 to ≈200 °C. This inspires the design of a lightweight, organic, elastic optical waveguide where the output energy is controlled by the operating temperature. The wide range of crystal flexibility expands the range of conditions for application of organic crystals as optical waveguides.

Dynamics of 5R-Tg Base Flipping in DNA Duplexes Based on Simulations─Agreement with Experiments and Beyond.

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping. Structural effects of the 5R-Tg epimers on the duplex DNA are herein studied using molecular dynamics together with reliable DFT based calculations. In comparison with the corresponding intact DNA, the cis-5R,6S-Tg epimer base causes little perturbation to the duplex DNA, and a barrier of 4.9 kcal mol–1 is obtained by meta-eABF for cis-5R,6S-Tg base flipping out of the duplex DNA, comparable to the 5.4 kcal mol–1 obtained for the corresponding thymine flipping in intact DNA. For the trans-5R,6R-Tg epimer, three stable local structures were identified, of which the most stable disrupts the Watson–Crick hydrogen-bonded G5/C20 base pair, leading to conformational distortion of the duplex. Interestingly, the relative barrier height of the 5R-Tg flipping is only 1.0 kcal mol–1 for one of these trans-5R,6R-Tg epimers. Water bridge interactions were identified to be essential for 5R-Tg flipping. The study clearly demonstrates the occurrence of partial trans-5R,6R-Tg epimer flipping in solution.

DNA kinks behavior in the potential pit-trap

<abstract> <p>For better understanding the role of dynamic factors in the DNA functioning, it is important to study the internal mobility of DNA and, in particular, the movement of nonlinear conformational distortions -kinks along the DNA chains. In this work, we study the behavior of the kinks in the pPF1 plasmid containing two genes of fluorescent proteins (EGFP and mCherry). To simulate the movement, two coupled nonlinear sine-Gordon equations that describe the angular oscillations of nitrogenous bases in the main and complementary chains and take into account the effects of dissipation and the action of a constant torsion field. To solve the equations, approximate methods such as the quasi-homogeneous approximation, the mean field method, and the block method, were used. The obtained solutions indicate that two types of kinks moving along the double strand can be formed in any part of the plasmid. The profiles of the potential fields in which these kinks are moving are calculated. The results of the calculations show that the lowest energy required for the kink formation, corresponds to the region located between the genes of green and red proteins (EGFP and mCherry). It is shown that it is in this region a pit trap is located for both kinks. Trajectories of the kinks in the pit-trap and nearby are constructed. It is shown that there are threshold values of the torsion field, upon reaching which the kinks behavior changes dramatically: there is a transition from cyclic motion inside the pit-trap to translational motion and exit from the potential pit-trap.</p> </abstract>

A Low Distortion Mesh Parameterization Mapping Method Based on Proxy Function and Combined Newton

To address the issues of low efficiencies and serious mapping distortions in current mesh parameterization methods, we present a low distortion mesh parameterization mapping method based on proxy function and combined Newton’s method in this paper. First, the proposed method calculates visual blind areas and distortion prone areas of a 3D mesh model, and generates a model slit. Afterwards, the method performs the Tutte mapping on the cut three-dimensional mesh model, measures the mapping distortion of the model, and outputs a distortion metric function and distortion values. Finally, the method sets iteration parameters, establishes a reference mesh, and finds the optimal coordinate points to get a convergent mesh model. When calculating mapping distortions, Dirichlet energy function is used to measure the isometric mapping distortion, and MIPS energy function is used to measure the conformal mapping distortion. To find the minimum value of the mapping distortion metric function, we use an optimal solution method combining proxy functions and combined Newton’s method. The experimental data show that the proposed method has high execution efficiency, fast descending speed of mapping distortion energy and stable optimal value convergence quality. When a texture mapping is performed, the texture is evenly colored, close laid and uniformly lined, which meets the standards in practical applications.

Molecular rationale for the impairment of the MexAB-OprM efflux pump by a single mutation in MexA

Efflux pumps of the Resistance-Nodulation-cell Division (RND) superfamily contribute to intrinsic and acquired resistance in Gram-negative pathogens by expelling chemically unrelated antibiotics with high efficiency. They are tripartite systems constituted by an inner-membrane-anchored transporter, an outer membrane factor protein, and a membrane fusion protein. Multimerization of the membrane fusion protein is an essential prerequisite for full functionality of these efflux pumps. In this work, we employed complementary computational techniques to investigate the stability of a dimeric unit of MexA (the membrane fusion protein of the MexAB-OprM RND efflux pump of Pseudomonas aeruginosa), and to provide a molecular rationale for the effect of the G72S substitution, which affects MexAB-OprM functionality by impairing the assembly of MexA. Our findings indicate that: i) dimers of this protein are stable in multiple µs-long molecular dynamics simulations; ii) the mutation drastically alters the conformational equilibrium of MexA, favouring a collapsed conformation that is unlikely to form dimers or higher order assemblies. Unveiling the mechanistic aspects underlying large conformational distortions induced by minor sequence changes is informative to efforts at interfering with the activity of this elusive bacterial weapon. In this respect, our work further confirms how molecular simulations can give important contribution and useful insights to characterize the mechanism of highly complex biological systems.

Photophysics of Azobenzene Constrained in a UiO Metal-Organic Framework: Effects of Pressure, Solvation and Dynamic Disorder.

Photophysical studies of chromophoric linkers in metal–organic frameworks (MOFs) are undertaken commonly in the context of sensing applications, in search of readily observable changes of optical properties in response to external stimuli. The advantages of the MOF construct as a platform for investigating fundamental photophysical behaviour have been somewhat overlooked. The linker framework offers a unique environment in which the chromophore is geometrically constrained and its structure can be determined crystallographically, but it exists in spatial isolation, unperturbed by inter‐chromophore interactions. Furthermore, high‐pressure studies enable the photophysical consequences of controlled, incremental changes in local environment or conformation to be observed and correlated with structural data. This approach is demonstrated in the present study of the trans‐azobenzene chromophore, constrained in the form of the 4,4’‐azobenzenedicarboxylate (abdc) linker, in a UiO topology framework. Previously unobserved effects of pressure‐induced solvation and conformational distortion on the lowest energy, nπ* transition are reported, and interpreted the light of crystallographic data. It was found that trans‐azobenzene remains non‐fluorescent (with a quantum yield less than 10−4) despite the prevention of trans‐cis isomerization by the constraining MOF structure. We propose that efficient non‐radiative decay is mediated by the local, pedal‐like twisting of the azo group that is evident as dynamic disorder in the crystal structure.

Conformational Adaptation of β-Peptide Foldamers for the Formation of Metal-Peptide Frameworks.

Metal-coordinated frameworks derived from small peptidic ligands have received much attention thanks to peptides' vast structural and functional diversity. Various peptides with partial conformational preferences have been used to build metal-peptide frameworks, however, the use of conformationally constrained β-peptide foldamers has not been explored yet. Herein we report the first metal-coordination-mediated assembly of β-peptide foldamers with 12-helical folding propensity. The coordination of Ag+ to the terminal pyridyl moieties afforded a set of metal-peptide frameworks with unique entangled topologies. Interestingly, formation of the network structures was accompanied by notable conformational distortions of the foldamer ligands. As the first demonstration of new metal-peptide frameworks built from modular β-peptide foldamers, we anticipate that this work will be an important benchmark for further structural evolution and mechanistic investigation.

Conformational Adaptation of β‐Peptide Foldamers for the Formation of Metal–Peptide Frameworks

AbstractMetal‐coordinated frameworks derived from small peptidic ligands have received much attention thanks to peptides’ vast structural and functional diversity. Various peptides with partial conformational preferences have been used to build metal–peptide frameworks, however, the use of conformationally constrained β‐peptide foldamers has not been explored yet. Herein we report the first metal‐coordination‐mediated assembly of β‐peptide foldamers with 12‐helical folding propensity. The coordination of Ag+ to the terminal pyridyl moieties afforded a set of metal–peptide frameworks with unique entangled topologies. Interestingly, formation of the network structures was accompanied by notable conformational distortions of the foldamer ligands. As the first demonstration of new metal–peptide frameworks built from modular β‐peptide foldamers, we anticipate that this work will be an important benchmark for further structural evolution and mechanistic investigation.

Thermally Activated Delayed Fluorescence Enabled by Reversed Conformational Distortion for Blue Emitters.

In this work, we present for the first time a general strategy via molecular reversed conformational distortion for thermally activated delayed fluorescence (TADF). A model purely organic compound named BNNIO with a common fluorophore flexibly linked to benzene by an oxygen atom is rationally designed and successfully synthesized. Moreover, the rate constant of reverse intersystem crossing reaches 2.34 × 104 s-1 as determined by transient spectroscopy. As a result, TADF emission of BNNIO is observed with a photoluminescence quantum yield of 90.72% and a lifetime of 84.76 μs at 415 nm. This universal regulation strategy undoubtedly opens a new avenue for the development of novel purely organic blue light-emitting materials.

Surface-Mediated Ring-Opening and Porphyrin Deconstruction via Conformational Distortion

The breakdown of macrocyclic compounds is of utmost importance in manifold biological and chemical processes, usually proceeding via oxygenation-induced ring-opening reactions. Here, we introduce a surface chemical route to selectively break a prototypical porphyrin species, cleaving off one pyrrole unit and affording a tripyrrin derivative. This pathway, operational in an ultrahigh vacuum environment at moderate temperature is enabled by a distinct molecular conformation achieved via the specific interaction between the porphyrin and its copper support. We provide an atomic-level characterization of the surface-anchored tripyrrin, its reaction intermediates, and byproducts by bond-resolved atomic force microscopy, unequivocally identifying the molecular skeletons. The ring-opening is rationalized by the distortion reducing the macrocycle's stability. Our findings open a route to steer ring-opening reactions by conformational design and to study intriguing tetrapyrrole catabolite analogues on surfaces.

Synthesis and characterization of new metal complexes containing Triazino[5,6–b]indole moiety: In vitro DNA and HSA binding studies

The present study reports the synthesis, structural characterization of Ni(II) (1,3) and Cu(II) (2,4) metal complexes of Schiff-base (L) derived from 5H-[1,2,4]triazino[5,6-b]indol-3-amine and salicylaldehyde moiety. The coordination sphere of Cu(II)/Ni(II) was completed by tethering secondary ligand 2,2′–Bipyridine and 1,10 phenanthroline to obtain the final complexes 1–4, respectively. The spectral analysis of complexes 1 and 3 suggested square planar geometry while complexes 2 and 4 acquire the octahedral geometry around the metal centers. In vitro DNA binding profiles of the newly synthesized metal complexes 1–4 with calf thymus DNA (CT DNA) were explored by employing electronic absorption titrations and fluorescence spectral studies. The results revealed that complexes 1–4 bind to DNA through electrostatic surface binding mode along with partial intercalation in the minor groove. Moreover, complexes 3 and 4 have stronger DNA binding propensity with higher intrinsic binding constant Kb values of 1.9 × 104 and 4.8 × 104 M–1, respectively. Additionally, HSA binding studies of ligand L and metal complexes 1–4 support the static quenching mechanism and alterations in the microenvironment around Trp–214 residues causing conformational distortions in the HSA secondary structure. Furthermore, molecular docking studies of complexes 3 and 4 with DNA and HSA confirms that both specifically binds in G–C rich regions of the DNA minor groove and subdomain IIA pocket of HSA near the Trp–214 residue.