Conformational Degrees Of Freedom Research Articles

Efficient and accurate binding free energy calculation of Aβ9-40 protofilament propagation.

Self-assembled aggregation of peptides and proteins into regular amyloid fibrils is associated with several neurodegenerative diseases. In case of Alzheimer's disease proteolytic cleavage products of the amyloid precursor protein form pathological amyloid-beta fibrils in a nucleation and propagation phase. The molecular details and thermodynamic driving forces of amyloid formation are not well understood, but are of high relevance for potential pharmacological interference. We used atomistic binding free energy simulations to calculate the free energy of protofilament propagation by an additional Aβ9-40 peptide binding to the protofilament tip. It requires sampling of relevant conformational transitions which is challenging since the monomeric Aβ9-40 peptide is intrinsically disordered. However, the convergence of umbrella simulations can be enhanced by applying additional restraining potentials on the axial, orientational and conformational degrees of freedom. The improved convergence leads to a much closer agreement with experimental binding free energy data compared to unrestrained umbrella sampling. Moreover, the restraining approach results in a separation of contributions to the total binding free energy. The calculated contributions indicate that the free energy change associated with the restriction of conformational freedom upon propagation makes a large opposing contribution of higher magnitude than the total binding free energy. Finally, optimization of the approach leads to further significant reduction of the computational demand which is crucial for systematic studies on mutations, denaturants and inhibitors in the fibril propagation step.

Amplifying Nanoparticle Reinforcement through Low Volume Topologically Controlled Chemical Coupling.

We present a streamlined method to covalently bond hydroxylated carbon nanotubes (CNOH) within a polyphenol matrix, all achieved through a direct, solvent-free process. Employing an extremely small concentration of CNOH (0.01% w/w) along with topologically contrasting linkers led to a maximum of 5-fold increase in modulus and a 25% enhancement in tensile strength compared to the unaltered matrix, an order of magnitude greater reinforcement (w/w) compared to state-of-the-art melt-processed nanocomposites. Through dynamic mechanical analysis, low field solid-state nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we uncovered the profound influence of linker's conformational degrees of freedom on the segmental dynamics and therefore the material's properties.

Novel Lipophilic Hydroxamates Based on Spirocarbocyclic Hydantoin Scaffolds with Potent Antiviral and Trypanocidal Activity.

Flaviviridae infections, such as those caused by hepatitis C (HCV) and dengue viruses (DENVs), represent global health risks. Infected people are in danger of developing chronic liver failure or hemorrhagic fever, both of which can be fatal if not treated. The tropical parasites Trypanosoma brucei and Trypanosoma cruzi cause enormous socioeconomic burdens in Sub-Saharan Africa and Latin America. Anti-HCV chemotherapy has severe adverse effects and is expensive, whereas dengue has no clinically authorized treatment. Antiparasitic medicines are often toxic and difficult to administer, and treatment failures are widely reported. There is an urgent need for new chemotherapies. Based on our previous research, we have undertaken structural modification of lead compound V with the goal of producing derivatives with both antiviral and trypanocidal activity. The novel spirocarbocyclic-substituted hydantoin analogs were designed, synthesized, and tested for antiviral activity against three HCV genotypes (1b, 3a, 4a), DENV, yellow fever virus (YFV), and two trypanosome species (T. brucei, T. cruzi). The optimization was successful and led to compounds with significant antiviral and trypanocidal activity and exceptional selectivity. Several modifications were made to further investigate the structure-activity relationships (SARs) and confirm the critical role of lipophilicity and conformational degrees of freedom.

Unusual Aspects of Charge Regulation in Flexible Weak Polyelectrolytes.

This article reviews the state of the art of the studies on charge regulation (CR) effects in flexible weak polyelectrolytes (FWPE). The characteristic of FWPE is the strong coupling of ionization and conformational degrees of freedom. After introducing the necessary fundamental concepts, some unconventional aspects of the the physical chemistry of FWPE are discussed. These aspects are: (i) the extension of statistical mechanics techniques to include ionization equilibria and, in particular, the use of the recently proposed Site Binding-Rotational Isomeric State (SBRIS) model, which allows the calculation of ionization and conformational properties on the same foot; (ii) the recent progresses in the inclusion of proton equilibria in computer simulations; (iii) the possibility of mechanically induced CR in the stretching of FWPE; (iv) the non-trivial adsorption of FWPE on ionized surfaces with the same charge sign as the PE (the so-called "wrong side" of the isoelectric point); (v) the influence of macromolecular crowding on CR.

Prediction of Electronic Properties of Radical-Containing Polymers at Coarse-Grained Resolutions

The properties of soft electronic materials depend on the coupling of electronic and conformational degrees of freedom over a wide range of spatiotemporal scales. The description of such properties requires multiscale approaches capable of, at the same time, accessing electronic properties and sampling the conformational space of soft materials. This could in principle be realized by connecting the coarse-grained (CG) methodologies required for adequate conformational sampling to conformationally averaged electronic property distributions via backmapping to atomistic-resolution level models and repeated quantum-chemical calculations. Computational demands of such approaches, however, have hindered their application in high-throughput computer-aided soft materials discovery. Here, we present a method that, combining machine learning and CG techniques, can replace traditional backmapping-based approaches without sacrificing accuracy. We illustrate the method for an emerging class of soft electronic materials, namely, nonconjugated, radical-containing polymers, promising materials for all-organic energy storage. Supervised machine learning models are trained to learn the dependence of electronic properties on polymer conformation at CG resolutions. We then parametrize CG models that retain electronic structure information, simulate CG condensed phases, and predict the electronic properties of such phases solely from the CG degrees of freedom. We validate our method by comparing it against a full backmapping-based approach and find good agreement between both methods. This work demonstrates the potential of the proposed method to accelerate multiscale workflows and provides a framework for the development of CG models that retain electronic structure information.

2D-Self-Assembled Organic Materials in Undoped Hole Transport Bilayers for Efficient Inverted Perovskite Solar Cells.

Interfaces between photoactive perovskite layer and selective contacts play a key role in the performance of perovskite solar cells (PSCs). The properties of the interface can be modified by the introduction of molecular interlayers between the halide perovskite and the transporting layers. Herein, two novel structurally related molecules, 1,3,5-tris(α-carbolin-6-yl)benzene (TACB) and the hexamethylated derivative of truxenotris(7-azaindole) (TTAI), are reported. Both molecules have the ability to self-assemble through reciprocal hydrogen bond interactions, but they have different degrees of conformational freedom. The benefits of combining these tripodal 2D-self-assembled small molecular materials with well-known hole transporting layers (HTLs), such as PEDOT:PSS and PTAA, in PSCs with inverted configuration are described. The use of these molecules, particularly the more rigid TTAI, enhanced the charge extraction efficiency and reduced the charge recombination. Consequently, an improved photovoltaic performance was achieved in comparison to the devices fabricated with the standard HTLs.

Conformational degrees of freedom and stability of splay-bend ordering in the limit of a very strong planar anchoring.

We study the self-organization in a monolayer (a two-dimensional system) of flexible planar trimer particles. The molecules are made up of two mesogenic units linked by a spacer, all of which are modeled as hard needles of the same length. Each molecule can dynamically adopt two conformational states: an achiral bent-shaped (cis-) and a chiral zigzag (trans-) one. Using constant pressure Monte Carlo simulations and Onsager-type density functional theory (DFT), we show that the system consisting of these molecules exhibits a rich spectrum of liquid crystalline phases. The most interesting observation is the identification of stable smectic splay-bend (S_{SB}) and chiral smectic-A (S_{A}^{*}) phases. The S_{SB} phase is also stable in the limit, where only cis- conformers are allowed. The second phase that occupies a considerable portion of the phase diagram is S_{A}^{*} with chiral layers, where the chirality of the neighboring layers is of opposite sign. The study of the average fractions of the trans- and cis- conformers in various phases shows that while in the isotropic phase all fractions are equally populated, the S_{A}^{*} phase is dominated by chiral conformers (zigzag), but the achiral conformers win in the smectic splay-bend phase. To clarify the possibility of stabilization of the nematic splay-bend (N_{SB}) phase for trimers, the free energy of the N_{SB} and S_{SB} phases is calculated within DFT for the cis- conformers, for densities where simulations show stable S_{SB}. It turns out that the N_{SB} phase is unstable away from the phase transition to the nematic phase, and its free energy is always higher than that of S_{SB}, down to the transition to the nematic phase, although the difference in free energies becomes extremely small when approaching the transition.

Revealing the Key Packing Features Determining the Stability of Peptide Bilayer Membrane.

Short surfactant-like amphiphilic peptide, A3K, resembling a surfactant with a hydrophobic tail (A3) and a polar headgroup (K), is experimentally determined to form a membrane. Although the peptides are known to exist as β-strands, the exact packing architecture stabilizing the membrane is unknown. Earlier simulation studies have reported successful packing configurations through trial and error. In this work, we present a systematic protocol to identify the best peptide configurations for different packing patterns. The influence of stacking peptides in square and hexagonal packing geometry with the neighboring peptides in parallel and antiparallel orientations was explored. The best peptide configurations were determined from the free energy of bringing 2-4 peptides together as a bundle that can be stacked into a membrane. The stability of the assembled bilayer membrane was further investigated through molecular dynamics simulation. The role of peptide tilting, interpeptide distance, the nature and the extent of interactions, and the conformational degrees of freedom on the stability of the membrane is discussed. The consistency with the experimental findings suggests hexagonal antiparallel as the most relevant molecular architecture.

Molecular Theory: A Tool for Predicting the Outcome of Self-Assembly of Polymers, Nanoparticles, Amphiphiles, and Other Soft Materials.

The supramolecular organization of soft materials, such as colloids, polymers, and amphiphiles, results from a subtle balance of weak intermolecular interactions and entropic forces. This competition can drive the self-organization of soft materials at the nano-/mesoscale. Modeling soft-matter self-assembly requires, therefore, considering a complex interplay of forces at the relevant length scales without sacrificing the molecular details that define the chemical identity of the system. This mini-review focuses on the application of a tool known as molecular theory to study self-assembly in different types of soft materials. This tool is based on extremizing an approximate free energy functional of the system, and, therefore, it provides a direct, computationally affordable estimation of the stability of different self-assembled morphologies. Moreover, the molecular theory explicitly incorporates structural details of the chemical species in the system, accounts for their conformational degrees of freedom, and explicitly includes their chemical equilibria. This mini-review introduces the general ideas behind the theoretical formalism and discusses its advantages and limitations compared with other theoretical tools commonly used to study self-assembled soft materials. Recent application examples are discussed: the self-patterning of polyelectrolyte brushes on planar and curved surfaces, the formation of nanoparticle (NP) superlattices, and the self-organization of amphiphiles into micelles of different shapes. Finally, prospective methodological improvements and extensions (also relevant for related theoretical tools) are analyzed.

Hazardous Shortcuts in Standard Binding Free Energy Calculations.

Calculating the standard binding free energies of protein-protein and protein-ligand complexes from atomistic molecular dynamics simulations in explicit solvent is a problem of central importance in computational biophysics. A rigorous strategy for carrying out such calculations is the so-called "geometrical route". In this method, two molecular objects are progressively separated from one another in the presence of orientational and conformational restraints serving to control the change in configurational entropy that accompanies the dissociation process, thereby allowing the computations to converge within simulations of affordable length. Although the geometrical route provides a rigorous theoretical framework, a tantalizing computational shortcut consists of simply leaving out such orientational and conformational degrees of freedom during the separation process. Here the accuracy and convergence of the two approaches are critically compared in the case of two protein-ligand complexes (Abl kinase-SH3:p41 and MDM2-p53:NVP-CGM097) and three protein-protein complexes (pig insulin dimer, SARS-CoV-2 spike RBD:ACE2, and CheA kinase-P2:CheY). The results of the simulations that strictly follow the geometrical route match the experimental standard binding free energies within chemical accuracy. In contrast, simulations bereft of geometrical restraints converge more poorly, yielding inconsistent results that are at variance with the experimental measurements. Furthermore, the orientational and positional time correlation functions of the protein in the unrestrained simulations decay over several microseconds, a time scale that is far longer than the typical simulation times of the geometrical route, which explains why those simulations fail to sample the relevant degrees of freedom during the separation process of the complexes.

Cooperative Intramolecular Dynamics Control the Chain-Length-Dependent Glass Transition in Polymers

The glass transition is a long-standing unsolved problem in materials science. For polymers, our understanding of glass-formation is particularly poor due to the added complexity of chain connectivity and flexibility; structural relaxation of polymers thus involves a complex interplay between intra- and inter-molecular cooperativity. Here we study how the glass transition temperature Tg varies with molecular weight M for different polymer chemistries and chain flexibilities. We find that Tg(M) is controlled by the average mass (or volume) per conformational degree of freedom, and that a `local' molecular relaxation (involving a few conformers) controls the larger-scale cooperative alpha relaxation responsible for Tg. We propose that dynamic facilitation where a `local' relaxation facilitates adjacent relaxations, leading to hierarchical dynamics, can explain our observations including logarithmic Tg(M) dependences. Our study provides a new understanding of molecular relaxations and the glass transition in polymers, which paves the way for predictive design of polymers based on monomer-scale metrics.

Optimizing the Calculation of Free Energy Differences in Nonequilibrium Work SQM/MM Switching Simulations.

A key step during indirect alchemical free energy simulations using quantum mechanical/molecular mechanical (QM/MM) hybrid potential energy functions is the calculation of the free energy difference ΔAlow→high between the low level (e.g., pure MM) and the high level of theory (QM/MM). A reliable approach uses nonequilibrium work (NEW) switching simulations in combination with Jarzynski’s equation; however, it is computationally expensive. In this study, we investigate whether it is more efficient to use more shorter switches or fewer but longer switches. We compare results obtained with various protocols to reference free energy differences calculated with Crooks’ equation. The central finding is that fewer longer switches give better converged results. As few as 200 sufficiently long switches lead to ΔAlow→high values in good agreement with the reference results. This optimized protocol reduces the computational cost by a factor of 40 compared to earlier work. We also describe two tools/ways of analyzing the raw data to detect sources of poor convergence. Specifically, we find it helpful to analyze the raw data (work values from the NEW switching simulations) in a quasi-time series-like manner. Principal component analysis helps to detect cases where one or more conformational degrees of freedom are different at the low and high level of theory.

Symmetry-Adapted Restraints for Binding Free Energy Calculations.

Binding free energy calculations rely critically on a precise definition of the bound state and well-designed ligand restraints to ensure that binding free energy calculations converge rapidly and yield estimates of well-defined thermodynamic quantities. The distance-to-bound-configuration (DBC) is a single variable that can precisely delineate the bound state of a ligand including translational, rotational and conformational degrees of freedom and has been successfully used to capture binding modes with complex geometries. DBC is defined as the root-mean-square deviation (RMSD) of ligand coordinates in the frame of reference of the binding site. In the special case where the ligand features symmetry-equivalent atoms, a standard RMSD arbitrarily distinguishes equivalent poses, mixing equivalent and nonequivalent degrees of freedom, and preventing the precise delineation of the bound state ensemble, which negates the benefits of defining a flat-bottom binding restraint. To remedy this, we introduce a symmetry-adapted DBC coordinate where the RMSD is minimized over permutations of equivalent ligand atoms. This coordinate is implemented in a portable software library, the Collective Variables Module. We tested the approach by computing the absolute binding free energy of benzene to the engineered site of a mutant lysozyme (L99A/M102H) using alchemical free energy perturbation. We found that the symmetry-adapted restraint leads to well-behaved convergence of both the decoupling free energy in the binding site and the restrained free energy in the gas phase, recovering the affinity computed using a classic center-of-mass restraint. Thus, symmetry-adapted DBC seamlessly generalizes the benefits of DBC restraints to the case of symmetric ligands. The underlying symmetric RMSD coordinate can also be used for analyzing or biasing simulations in other contexts than affinity predictions.

Folding Free Energy Surfaces from Differential Scanning Calorimetry.

Protein folding/unfolding processes involve a large number of weak, non-covalent interactions and are more appropriately described in terms of the movement of a point representing protein conformation in a plot of internal free energy versus conformational degrees of freedom. While these energy landscapes have an astronomically large number of dimensions, it has been shown that many relevant aspects of protein folding can be understood in terms of their projections onto a few relevant coordinates. Remarkably, such low-dimensional free energy surfaces can be obtained from experimental DSC data using suitable analytical models. Here, we describe the experimental procedures to be used to obtain the high-quality DSC data that are required for free-energy surface analysis.

Molecular Conformation in Charge Tunneling across Large-Area Junctions.

Self-assembled monolayers are predicated on thermodynamic equilibrium; hence, their properties project accessible relaxation pathways. Herein, we demonstrate that charge tunneling correlates with conformational degrees of freedom(s). Results from open chain and cyclic head groups show that, as expected, distribution in tunneling data correlates with the orientation of the head group, akin to the odd-even effect and more importantly the degree of conformational freedom, but fluctuates with applied bias. Trends in nature of distributions in current density illuminate the need for higher statistical moments in understanding these rather dynamic systems. We employ skewness, kurtosis, and estimation plots to show that the conformational degree of freedom in the head group significantly amplifies the odd-even effect and may lead to enhanced or perturbed tunneling based on whether the head group is on an odd- or even-parity spacer.

Optical spectroscopy study of the interaction between curcumin and acrylic polymers

This paper presents the results of a study conducted on the interaction between curcumin, a compound with several biomedical applications in traditional and modern medicine, and the acrylic polymers poly(methyl methacrylate), poly(ethyl methacrylate), and poly(n-butyl methacrylate), through photophysical experiments in curcumin/acrylic polymers casting films. Optical absorption intensity at ~340 nm increases relatively to its maximum at ~417 nm when the amount of curcumin in the polymeric film decreases, due to a significant change in the concentration of the isomers cis- or trans-form of curcumin, regardless of the acrylic polymer. Fluorescence (FL) spectra of the films depend on the curcumin concentration in the matrix with well-resolved line shape. They show two distinct bands, one at ~525 nm, for higher curcumin concentration (5.00 mmol.L-1), related to the aggregated curcumin species, and another at ~465 nm, for lower concentration of curcumin (0.10 mmol.L-1), related to the effects of the solvent on the conformational structure of the curcumin molecule and the presence of the trans-form of curcumin. The parameter Kagg, related to the contribution of the aggregated curcumin, shows the influence of the polymeric lateral chain length of the matrix in the de-aggregation of the curcumin. The Huang-Rhys factor indicates that curcumin aggregated species are conformationally more stable, and that the isolate species depends on the chemical environment and the matrix/curcumin interaction, decreasing its conformational degrees of freedom. Arrhenius plots, obtained via FL experiment in function of the sample temperature, show that, for higher curcumin concentration, the value for the relaxation energy process is not well defined, due the decrease in the interaction between the matrix and the curcumin molecules. With these results, it is possible to infer that the interaction matrix/curcumin must occur via lateral chemical alkyl groups.

Development of functionalized nanocrystalline cellulose-based polyelectrolytes with high water uptake

Dicarboxylate nanocrystalline cellulose (DCNC) polyelectrolytes were prepared from nanocrystalline cellulose (NCC) by introducing carboxylate units at the C-2 and C-3 positions of a glucose moiety through a two-step selective oxidation process. The polyelectrolyte nature of the DCNC was investigated by measuring the water uptake capacity with a customized ion exchange system. The equilibrium water uptake capacity of DCNC was almost ten times greater than that of conventional C-6 functionalized monocarboxylated NCC. The conversion of NCC to DCNC ensured the presence of a large number of dissociable electrolytic ions and high degrees of conformational freedom in the material to generate high osmotic pressure. Conductivity and dynamic light-scattering measurements were performed to relate the water uptake capacity with the chemical and structural changes of the polyelectrolytes. Furthermore, it was observed that the ionic strength of the solution played a critical role in controlling the water uptake capacity of the material. Polyelectrolytes (PEs) with high water uptake prepared from cellulose-type polysaccharides are promising because of their excellent biodegradability. In this work, utilizing a two-step selective oxidation process a new type dicarboxylate nanocrystalline cellulose (DCNC) PE was prepared. Carboxylate units were introduced at the C-2 and C-3 positions of a glucose moiety to ensure the presence of a large number of dissociable electrolytic ions. It was observed that the equilibrium water uptake capacity of the prepared DCNC was almost ten times greater than that of conventional C-6 functionalized monocarboxylated nanocrystalline cellulose.

Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding

Summary Because of proteins’ many degrees of conformational freedom, programming protein folding dynamics, overall elasticity, and motor functions remains an elusive objective. Instead, smaller and simpler objects, such as synthetic foldamers, may be amenable to design. However, little is known about their mechanical performance. Here, we show that reducing molecular size may not compromise mechanical properties. We report that helical aromatic oligoamides as small as 1 nm possess outstanding elasticity and outperform most natural helices. Using single-molecule force spectroscopy, we characterize their folding trajectories and intermediate states. We show that they cooperatively and reversibly unwind at high forces. They extend up to 3.8 times their original length and rewind against considerable forces on a timescale of 10 μs. Pulling and relaxing cycles follow the same trace up to a very high loading rate, indicating that the mechanical energy accumulated during the stretching does not dissipate and is immediately reusable.

Electronic structure modelling of the edge-functionalisation of graphene by MnxOy particles.

The use of graphenic carbon is attractive as a basal or intermediate support for catalytic particles in advanced catalytic electrodes. This popularity is motivated by its excellent electrical properties and ability to form foliated conformal coatings of exceptional surface area and flexibility. Surface- and edge-functionalisation of graphene sheets affords diverse routes to the covalent attachment of candidate catalytic species. Of particular interest to advanced water oxidation is the possibility of covalent attachment of MnxOy species partially recapitulating the chemistry of the Mn4O5Ca active site of Photosystem II (PSII), which achieves the four-electron oxidation of water under physiological conditions. Here, we report aperiodic density functional theory (DFT) investigations of candidate attachment geometries for a variety of manganese oxide particles to graphene sheets. We find that the flexibility of graphene sheets as well as the conformational degrees of freedom of candidate edge functionalisation permits a large variety of realistic attachment geometries that can act as attachment sites for molecular manganese-oxide species or nuclei for the growth of periodic manganese oxides. We find that substantially simplified models of graphene attachment afford an excellent compromise between computational efficiency, tractability, and accuracy, and characterise the accuracy of these models in detail.

Probing Allosteric Mechanism with Long-Range Rigidity Transmission Across Protein Networks.

Allosteric transmission refers to regulation of protein function at a distance. "Allostery" involves regulation and/or signal transduction induced by a perturbation event. Allostery, which has been coined the "second secret of life," is a fundamental property of most dynamics proteins. Most of critical questions surrounding allostery are largely unresolved. One of the key puzzles is to describe the physical mechanism of distant coupled conformational change. Another hot research area surrounding allostery is detection of allosteric pathways or regions (residues) in the protein that are the most critical for transmission of allosteric information. Using techniques inspired by mathematical rigidity theory and mechanical linkages, we have previously proposed a mechanistic model and description of allosteric transmission and an accompanying computational method, the Rigidity Transmission Allostery (RTA) algorithm. The RTA algorithm and method are designed to predict if mechanical perturbation of rigidity, for example, due to ligand binding, at one site of the protein can transmit and propagate across a protein structure and in turn cause a change in available conformational degrees of freedom and a change in conformation at a second distant site, equivalently resulting in allosteric transmission. The RTA algorithm is computationally very fast and can rapidly scan many unknown sites for allosteric transmission, identifying potential novel allosteric sites and quantify their allosteric effect. In this chapter we will discuss the rigidity-based mechanistic model of allosteric communication. As a case illustrativestudy, we will demonstrateRTA analysis on a G protein coupled receptor (GPCR) human adenosine A2A receptor. Our method gives important implications and a novel prospective for general mechanistic description of allostericcommunication.