Side-chain Motions Research Articles

Bidirectional modulation of HIF-2 activity through chemical ligands.

Hypoxia-inducible factor-2 (HIF-2) is a heterodimeric transcription factor formed through dimerization between an oxygen-sensitive subunit HIF-2α subunit and its obligate partner subunit ARNT. Enhanced HIF-2 activity drives some cancers, while reduced activity causes anemia in chronic kidney disease. Therefore, modulation of HIF-2 activity via direct-binding ligands could provide many new therapeutic benefits. Here, we explored HIF-2α chemical ligands using combined crystallographic, biophysical, and cell-based functional studies. We found chemically unrelated antagonists to employ the same mechanism of action. Their binding displaced residue M252 from inside the HIF-2α PAS-B pocket toward the ARNT subunit to weaken heterodimerization. We also identified first-in-class HIF-2α agonists and found they significantly displaced pocket residue Y281. Its dramatic side-chain movement increases heterodimerization stability and transcriptional activity. Our findings show that despite binding to the same HIF-2α PAS-B pocket, ligands can manifest as inhibitors versus activators by mobilizing different pocket residues to allosterically alter HIF-2α-ARNT heterodimerization.

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.

Molecular simulations are a valuable tool for studying biomolecular motions and thermodynamics. However, such motions can be slow compared to simulation time scales, yet critical. Specifically, adequate sampling of side chain motions in protein binding pockets is crucial for obtaining accurate estimates of ligand binding free energies from molecular simulations. The time scale of side chain rotamer flips can range from a few ps to several hundred ns or longer, particularly in crowded environments like the interior of proteins. Here, we apply a mixed nonequilibrium candidate Monte Carlo (NCMC)/molecular dynamics (MD) method to enhance sampling of side chain rotamers. The NCMC portion of our method applies a switching protocol wherein the steric and electrostatic interactions between target side chain atoms and the surrounding environment are cycled off and then back on during the course of a move proposal. Between NCMC move proposals, simulation of the system continues via traditional molecular dynamics. Here, we first validate this approach on a simple, solvated valine-alanine dipeptide system and then apply it to a well-studied model ligand binding site in T4 lysozyme L99A. We compute the rate of rotamer transitions for a valine side chain using our approach and compare it to that of traditional molecular dynamics simulations. Here, we show that our NCMC/MD method substantially enhances side chain sampling, especially in systems where the torsional barrier to rotation is high (≥10 kcal/mol). These barriers can be intrinsic torsional barriers or steric barriers imposed by the environment. Overall, this may provide a promising strategy to selectively improve side chain sampling in molecular simulations.

Interplay of cysteine exposure and global protein dynamics in small-molecule recognition by a regulator of G-protein signaling protein.

Regulator of G protein signaling (RGS) proteins play a pivotal role in regulation of G protein-coupled receptor (GPCR) signaling and are therefore becoming an increasingly important therapeutic target. Recently discovered thiadiazolidinone (TDZD) compounds that target cysteine residues have shown different levels of specificities and potencies for the RGS4 protein, thereby suggesting intrinsic differences in dynamics of this protein upon binding of these compounds. In this work, we investigated using atomistic molecular dynamics (MD) simulations the effect of binding of several small-molecule inhibitors on perturbations and dynamical motions in RGS4. Specifically, we studied two conformational models of RGS4 in which a buried cysteine residue is solvent-exposed due to side-chain motions or due to flexibility in neighboring helices. We found that TDZD compounds with aromatic functional groups perturb the RGS4 structure more than compounds with aliphatic functional groups. Moreover, small-molecules with aromatic functional groups but lacking sulfur atoms only transiently reside within the protein and spontaneously dissociate to the solvent. We further measured inhibitory effects of TDZD compounds using a protein-protein interaction assay on a single-cysteine RGS4 protein showing trends in potencies of compounds consistent with our simulation studies. Thermodynamic analyses of RGS4 conformations in the apo-state and on binding to TDZD compounds revealed links between both conformational models of RGS4. The exposure of cysteine side-chains appears to facilitate initial binding of TDZD compounds followed by migration of the compound into a bundle of four helices, thereby causing allosteric perturbations in the RGS/Gα protein-protein interface.

Solid polymer electrolytes based on polystyrene‐polyether block copolymers having branched ether structure

To obtain solid polymer electrolytes (SPEs) having high ionic conductivity together with mechanical integrity, we have synthesized polystyrene (PSt)‐polyether (PE) diblock copolymers via one‐pot anionic polymerization. The PSt block is expected to aggregate to act as hard fillers in the SPE to enhance the mechanical property. The PE block consists of random copolymer (P(EO‐r‐MEEGE)) of ethylene oxide (EO) and 2‐(2‐methoxyethoxy) ethyl glycidyl ether (MEEGE) in different molar ratios ([EO]/[MEEGE] = 100/0, 86/14, 75/25, 68/32, and 41/59). The introduction of the MEEGE moiety in PEO reduced the crystallinity of PEO, and the fast motion of the MEEGE side chain caused plasticization of the PE block, thereby contributing to the fast ion transport. SPEs were fabricated by mixing the obtained diblock copolymer (PSEx) and lithium bis(trifluoromethanesulfonyl) amide (LiTFSA) with [Li]/[O] = 0.05. Ionic conductivity of the obtained SPEs was dependent on the molar ratio of EO in the PE block (x) as well as the weight fraction of PE block (fPE) in the block copolymer. PSE0.86 (fPE = 0.65) exhibited high ionic conductivity (3.3 × 10−5 S cm−1 at 30°C; 1.1 × 10−4 S cm−1 at 60°C) comparable with that of P(EO‐r‐MEEGE) (PE0.85; fPE = 1.00) (9.8 × 10−5 S cm−1 at 30°C; 4.0 × 10−4 S cm−1 at 60°C).

Characterization of Internal Protein Dynamics and Conformational Entropy by NMR Relaxation.

Recent studies suggest that the fast timescale motion of methyl-bearing side chains may play an important role in mediating protein activity. These motions have been shown to encapsulate the residual conformational entropy of the folded state that can potentially contribute to the energetics of protein function. Here, we provide an overview of how to characterize these motions using nuclear magnetic resonance (NMR) spin relaxation methods. The strengths and limitations of several techniques are highlighted in order to assist with experimental design. Particular emphasis is placed on the practical aspects of sample preparation, data collection, data fitting, and statistical analysis. Additionally, discussion of the recently refined "entropy meter" is presented and its use in converting NMR observables to conformational entropy is illustrated. Taken together, these methods should yield new insights into the complex interplay between structure and dynamics in protein function.

Probing Protein Dynamics Using Multifield Variable Temperature NMR Relaxation and Molecular Dynamics Simulation.

Understanding the interplay between protein function and dynamics is currently one of the fundamental challenges of physical biology. Recently, a method using variable temperature solid-state nuclear magnetic resonance relaxation measurements has been proposed for the simultaneous measurement of 12 different activation energies reporting on distinct dynamic modes in the protein GB1. Here, we extend this approach to measure relaxation at multiple magnetic field strengths, allowing us to better constrain the motional models and to simultaneously evaluate the robustness and physical basis of the method. The data reveal backbone and side-chain motions, exhibiting low- and high-energy modes with temperature coefficients around 5 and 25 kJ·mol-1. The results are compared to variable temperature molecular dynamics simulation of the crystal lattice, providing further support for the interpretation of the experimental data in terms of molecular motion.

Tunable Stimuli‐Responsive Color‐Change Properties of Layered Organic Composites

AbstractStimuli‐responsive properties of soft materials originate from dynamic structure changes. Layered polydiacetylene (PDA) shows color‐change properties with the application of external stimuli, such as thermal and mechanical stresses. Layered organic materials possessing intercalation capabilities and dynamic properties have potentials for tuning their structures and properties by the intercalated guests. A variety of sensing and imaging devices can be developed by control of the stimuli responsivity. Here, the key structures, processes, and mechanisms for tuning the stimuli‐responsive color‐change properties of layered PDA are studied by in situ analyses with heating and cooling. The in situ analyses indicate that heating initiates thermal motion of the alkyl side chains of the PDA main chain in the host layers around 60 °C, regardless of the type of intercalated guests. Further heating induces torsion of the PDA main chain leading to color changes at different temperatures, depending on the types of the intercalated guest. Then, the layered structure is irreversibly deformed with lowering the crystallinity. The results indicate that the stimuli‐responsive color‐change properties are controlled by the rigidity of the layered structures consisting of the host layers and guests. The control strategy based on rigidity tuning can be applied to a variety of soft materials with stimuli responsivity.

Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations.

Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions.

Side chain length affects backbone dynamics in poly(3‐alkylthiophene)s

ABSTRACTCharge transport in conjugated polymers may be governed not only by the static microstructure but also fluctuations of backbone segments. Using molecular dynamics simulations, we predict the role of side chains in the backbone dynamics for regiorandom poly(3‐alkylthiophene‐2,5‐diyl)s (P3ATs). We show that the backbone of poly(3‐dodecylthiophene‐2‐5‐diyl) (P3DDT) moves faster than that of poly(3‐hexylthiophene‐2,5‐diyl) (P3HT) as a result of the faster motion of the longer side chains. To verify our predictions, we investigated the structures and dynamics of regiorandom P3ATs with neutron scattering and solid state NMR. Measurements of spin‐lattice relaxations (T1) using NMR support our prediction of faster motion for side chain atoms that are farther away from the backbone. Using small‐angle neutron scattering (SANS), we confirmed that regiorandom P3ATs are amorphous at about 300 K, although microphase separation between the side chains and backbones is apparent. Furthermore, quasi‐elastic neutron scattering (QENS) reveals that thiophene backbone motion is enhanced as the side chain length increases from hexyl to dodecyl. The faster motion of longer side chains leads to faster backbone dynamics, which in turn may affect charge transport for conjugated polymers. © 2018 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018, 56, 1193–1202

Targeting isoprenoid biosynthesis pathway in Staphylococcus lugdunensis: Comparative docking and simulation studies of conventional and allosteric sites

The current study establishes the use of in silico subtractive genomics approach, molecular docking and molecular dynamic (MD) simulation studies for identifying and inhibiting a potential therapeutic target protein involved in vital metabolic pathways and is therefore crucial for the survival of the human pathogen Staphylococcus lugdunensis. Filtering all the druggable target proteins based on cellular localization and functional annotation has led to the selection of farnesyl diphosphate synthase (Fds). Fds is the key enzyme involved in isoprenoid biosynthesis pathway. Homology model of the protein was generated via MODELLER and other web-based servers. Most reliable protein model selected on the basis of comparative analysis was used as an input for molecular docking studies performed using a total library of 374 compounds. Both conventional and allosteric binding sites were probed to assess the inhibitor binding potential. Among the studied compounds, non-bisphosphonate bisamidines, compound 160 (GOLD Score 79.8) and compound 193 (GOLD Score 87.84) were the top scoring compounds against the normal and allosteric binding pockets, respectively. MD simulations were applied further to explore the dynamic behaviour of both complexes in order to get an insight into structural and conformational changes induced upon ligand binding. MD simulation results revealed that the allosteric binding pocket was slightly more compact and stable when compared to the conventional binding pocket. Significant conformational changes including considerable side chain movements were observed in the binding site amino acid residues accompanied by rearrangement of the hydrogen bonding pattern in conventional and allosteric binding pockets.

Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy

Proteins have distinctive dynamical properties, characterized by the fluctuations of protein molecules among the different minima of their energy landscape. These fluctuations, progressively activated for temperature values larger than ~180 K, lead to a steep increase in the temperature dependence of all measurable dynamical properties. This phenomenon is known as Protein Dynamical Transition and, in spite of the intense studies due to its importance in protein function and to the relation with the fascinating fundamental thermodynamics of complex systems, many aspects of it are not yet clearly understood. Among these, the relationship with the properties of the external solvent and the molecular details of the involved protein motions still need further investigations.We report here a comparative study of the Dynamical Transition in a Protein-Glycerol-Water system, from two different points of view: i) Elastic Neutron Scattering (ENS), which gives the Mean Square Displacements of the hydrogen atoms of the protein and is particularly sensitive to side chain motions; ii) Fourier Transform Infrared Spectroscopy (FTIR) in the Amide regions, which is sensitive mainly to the properties of the backbone atoms of the protein. The obtained results show an almost superimposable thermal behavior of protein backbone (FTIR data) and side chains (ENS data). Thus, in our experimental conditions, the Protein Dynamical Transition emerges as a unique thermodynamic process related to the properties of the external Glycerol/Water medium and implying a general softening of the whole protein molecule (backbone and side chains), which is a prerequisite for protein function.

Transitions in DNA polymerase β μs-ms dynamics related to substrate binding and catalysis.

DNA polymerase β (pol β) plays a central role in the DNA base excision repair pathway and also serves as an important model polymerase. Dynamic characterization of pol β from methyl-TROSY 13C-1H multiple quantum CPMG relaxation dispersion experiments of Ile and Met sidechains and previous backbone relaxation dispersion measurements, reveals transitions in μs-ms dynamics in response to highly variable substrates. Recognition of a 1-nt-gapped DNA substrate is accompanied by significant backbone and sidechain motion in the lyase domain and the DNA binding subdomain of the polymerase domain, that may help to facilitate binding of the apoenzyme to the segments of the DNA upstream and downstream from the gap. Backbone μs-ms motion largely disappears after formation of the pol β–DNA complex, giving rise to an increase in uncoupled μs-ms sidechain motion throughout the enzyme. Formation of an abortive ternary complex using a non-hydrolyzable dNTP results in sidechain motions that fit to a single exchange process localized to the catalytic subdomain, suggesting that this motion may play a role in catalysis.

Dielectric Properties of Bio-Based Diphenolate Ester Epoxies.

Thermoset bio-based diglycidyl ether of diphenolate esters (DGEDP) exhibit comparable mechanical properties as petroleum-derived diglycidyl ether of bisphenol A (DGEBA), whereas DGEDP is derived from levulinic acid, a safe and readily renewable feedstock. To determine the potential replacement of DGEBA as dielectric materials, a series of DGEDP-esters (i.e., methyl, ethyl, propyl, and butyl esters) were synthesized and studied. Broadband dielectric spectroscopy revealed that DGEDP-propyl has the highest dielectric constant in the series, comparable to DGEBA. Differences in the dielectric properties of DGEDP-esters is attributed to the interplay of segmental, small local, and side-chain motions on one hand and free volume and steric hindrance on the other.

Crystal Structure of CYP2B6 in Complex with an Efavirenz Analog.

The over two dozen CYP2B structures of human, rabbit, and woodrat enzymes solved in the last decade have significantly enhanced our understanding of the structure-function relationships of drug metabolizing enzymes. More recently, an important role has emerged for halogen-π interactions in the CYP2B6 active site in substrate selectivity, explaining in part the preference for halogenated ligands as substrates. The mechanism by which such ligands interact with CYP2B enzymes involves conserved phenylalanine side chains, in particular F108, F115, or F297, in the active site, which form π bonds with halogens. To illustrate such halogen-π interactions using drugs that are major substrates of CYP2B6, we present here a crystal structure of CYP2B6 in complex with an analog of the widely used anti-HIV drug efavirenz, which contains a methyl group in place of the carbonyl oxygen. The chlorine of the efavirenz analog forms a π bond with the aromatic ring of F108, whereas the putative metabolism site on the distal end of the molecule is oriented towards the heme iron. The crystal structure showcases how CYP2B6 accommodates this important drug analog of considerable size in the active site by movement of various side chains without substantially increasing the active site volume. Furthermore, the CYP2B6-efavirenz analog complex provides a useful platform to investigate computationally as well as biophysically the effect of genetic polymorphisms on binding of the widely studied efavirenz.

Exploring the structural origins of cryptic sites on proteins

Molecular dynamics (MD) simulations of proteins reveal the existence of many transient surface pockets; however, the factors determining what small subset of these represent druggable or functionally relevant ligand binding sites, called "cryptic sites," are not understood. Here, we examine multiple X-ray structures for a set of proteins with validated cryptic sites, using the computational hot spot identification tool FTMap. The results show that cryptic sites in ligand-free structures generally have a strong binding energy hot spot very close by. As expected, regions around cryptic sites exhibit above-average flexibility, and close to 50% of the proteins studied here have unbound structures that could accommodate the ligand without clashes. Nevertheless, the strong hot spot neighboring each cryptic site is almost always exploited by the bound ligand, suggesting that binding may frequently involve an induced fit component. We additionally evaluated the structural basis for cryptic site formation, by comparing unbound to bound structures. Cryptic sites are most frequently occluded in the unbound structure by intrusion of loops (22.5%), side chains (19.4%), or in some cases entire helices (5.4%), but motions that create sites that are too open can also eliminate pockets (19.4%). The flexibility of cryptic sites frequently leads to missing side chains or loops (12%) that are particularly evident in low resolution crystal structures. An interesting observation is that cryptic sites formed solely by the movement of side chains, or of backbone segments with fewer than five residues, result only in low affinity binding sites with limited use for drug discovery.

Escape of a Small Molecule from Inside T4 Lysozyme by Multiple Pathways

The T4 lysozyme L99A mutant is often used as a model system to study small-molecule binding to proteins, but pathways for ligand entry and exit from the buried binding site and the associated protein conformational changes have not been fully resolved. Here, molecular dynamics simulations were employed to model benzene exit from its binding cavity using the weighted ensemble (WE) approach to enhance sampling of low-probability unbinding trajectories. Independent WE simulations revealed four pathways for benzene exit, which correspond to transient tunnels spontaneously formed in previous simulations of apo T4 lysozyme. Thus, benzene unbinding occurs through multiple pathways partially created by intrinsic protein structural fluctuations. Motions of several α-helices and side chains were involved in ligand escape from metastable microstates. WE simulations also provided preliminary estimates of rate constants for each exit pathway. These results complement previous works and provide a semiquantitative characterization of pathway heterogeneity for binding of small molecules to proteins.

Structural, morphological, electrical and electrochemical study on plasticized PVdF-HFP/PEMA blended polymer electrolyte for lithium polymer battery application

The compositional effect of blending plasticized poly (vinylidenefluoride-co-hexafluoropropylene) (PVdF-HFP) with different wt% of poly(ethyl methaacrylate) (PEMA) on its electrical properties was studied through AC impedance analysis. The maximum ionic conductivity of 2.14 × 10−2 S/cm at 303 K was found for 5 wt% of PEMA blended film which almost one order higher than the plasticized PVdF-HFP film with no blending (3.15 × 10−3 S/cm). However, blending of 10 wt% of PEMA dropped the conductivity to (5.12 × 10−4 S/cm). This drastic change in conductivity was explained in detail by X-Ray Diffraction (XRD), Fourier Transform Infrared Spectroscopy (FTIR) and Scanning Electron Microscope (SEM) analysis. The dielectric studies showed increase in side chain movements of the host polymer PVdF-HFP for 5 wt% of PEMA blending. However, this segmental motion was found hindered for 10 wt% of PEMA due to steric effect. TG-DTA shows the thermal stability of the plasticized polymer membrane to be increased for the addition of 5 wt% PEMA. Lithium metal polymer cell was made using the optimized blend membrane as an electrolyte with LiV3O8 as cathode and Li metal as anode. The lithium metal polymer cell was found to deliver the specific discharge capacity of 223 mAh/g at the second cycle.

Ion Channel Sensing: Are Fluctuations the Crux of the Matter?

The nonselective cation channel TRPV1 is responsible for transducing noxious stimuli into action potentials propagating through peripheral nerves. It is activated by temperatures greater than 43 °C, while remaining completely nonconductive at temperatures lower than this threshold. The origin of this sharp response, which makes TRPV1 a biological temperature sensor, is not understood. Here we used molecular dynamics simulations and free energy calculations to characterize the molecular determinants of the transition between nonconductive and conductive states. We found that hydration of the pore and thus ion permeation depends critically on the polar character of its molecular surface: in this narrow hydrophobic enclosure, the motion of a polar side-chain is sufficient to stabilize either the dry or wet state. The conformation of this side-chain is in turn coupled to the hydration state of four peripheral cavities, which undergo a dewetting transition at the activation temperature.

Transport-Relevant Protein Conformational Dynamics and Water Dynamics on Multiple Time Scales in an Archetypal Proton Channel: Insights from Solid-State NMR.

The influenza M2 protein forms a tetrameric proton channel that conducts protons from the acidic endosome into the virion by shuttling protons between water and a transmembrane histidine. Previous NMR studies have shown that this histidine protonates and deprotonates on the microsecond time scale. However, M2's proton conduction rate is 10-1000 s-1, more than 2 orders of magnitude slower than the histidine-water proton-exchange rate. M2 is also known to be conformationally plastic. To address the disparity between the functional time scale and the time scales of protein conformational dynamics and water dynamics, we have now investigated a W41F mutant of the M2 transmembrane domain using solid-state NMR. 13C chemical shifts of the membrane-bound peptide indicate the presence of two distinct tetramer conformations, whose concentrations depend exclusively on pH and hence the charge-state distribution of the tetramers. High-temperature 2D correlation spectra indicate that these two conformations interconvert at a rate of ∼400 s-1 when the +2 and +3 charge states dominate, which gives the first experimental evidence of protein conformational motion on the transport time scale. Protein 13C-detected water 1H T2 relaxation measurements show that channel water relaxes an order of magnitude faster than bulk water and membrane-associated water, indicating that channel water undergoes nanosecond motion in a pH-independent fashion. These results connect motions on three time scales to explain M2's proton-conduction mechanism: picosecond-to-nanosecond motions of water molecules facilitate proton Grotthuss hopping, microsecond motions of the histidine side chain allow water-histidine proton transfer, while millisecond motions of the entire four-helix bundle constitute the rate-limiting step, dictating the number of protons released into the virion.

Beneficial use of rotatable-spacer side-chains in alkaline anion exchange membranes for fuel cells

Rotatable spacer increases the motions of ionic side-chain to accelerate both ion and H2O transport during fuel cell operation.