Large Structural Fluctuations Research Articles

Energetic robustness to large scale structural fluctuations in a photosynthetic supercomplex

Photosynthetic organisms transport and convert solar energy with near-unity quantum efficiency using large protein supercomplexes held in flexible membranes. The individual proteins position chlorophylls to tight tolerances considered critical for fast and efficient energy transfer. The variability in protein organization within the supercomplexes, and how efficiency is maintained despite variability, had been unresolved. Here, we report on structural heterogeneity in the 2-MDa cyanobacterial PSI-IsiA photosynthetic supercomplex observed using Cryo-EM, revealing large-scale variances in the positions of IsiA relative to PSI. Single-molecule measurements found efficient IsiA-to-PSI energy transfer across all conformations, along with signatures of transiently decoupled IsiA. Structure based calculations showed that rapid IsiA-to-PSI energy transfer is always maintained, and even increases by three-fold in rare conformations via IsiA-specific chls. We postulate that antennae design mitigates structural fluctuations, providing a mechanism for robust energy transfer in the flexible membrane.

Molecular Dynamic Simulation Reveals Structure Differences in APOL1 Variants and Implication in Pathogenesis of Chronic Kidney Disease.

Background: According to observational studies, two polymorphisms in the apolipoprotein L1 (APOL1) gene have been linked to an increased risk of chronic kidney disease (CKD) in Africans. One polymorphism involves the substitution of two amino-acid residues (S342G and I384M; known as G1), while the other involves the deletion of two amino-acid residues in a row (N388 and Y389; termed G2). Despite the strong link between APOL1 polymorphisms and kidney disease, the molecular mechanisms via which these APOL1 mutations influence the onset and progression of CKD remain unknown. Methods: To predict the active site and allosteric site on the APOL1 protein, we used the Computed Atlas of Surface Topography of Proteins (CASTp) and the Protein Allosteric Sites Server (PASSer). Using an extended molecular dynamics simulation, we investigated the characteristic structural perturbations in the 3D structures of APOL1 variants. Results: According to CASTp’s active site characterization, the topmost predicted site had a surface area of 964.892 Å2 and a pocket volume of 900.792 Å3. For the top three allosteric pockets, the allostery probability was 52.44%, 46.30%, and 38.50%, respectively. The systems reached equilibrium in about 125 ns. From 0–100 ns, there was also significant structural instability. When compared to G1 and G2, the wildtype protein (G0) had overall high stability throughout the simulation. The root-mean-square fluctuation (RMSF) of wildtype and variant protein backbone Cα fluctuations revealed that the Cα of the variants had a large structural fluctuation when compared to the wildtype. Conclusion: Using a combination of different computational techniques, we identified binding sites within the APOL1 protein that could be an attractive site for potential inhibitors of APOL1. Furthermore, the G1 and G2 mutations reduced the structural stability of APOL1.

High Cycle Stability of Nanoporous Si Composites in All-solid-state Lithium-ion Batteries

Stress relaxation of Si with large structural fluctuations is a critical challenge for its practical application in lithium-ion batteries (LIBs). In this study, nanoporous Si particles, which are prepared by Mg2Si reduction of mesoporous SiO2 spheres, are applied as an anode active material for all-solid-state LIBs (ASSLIBs) with a Li3PS4 solid electrolyte. Nanoporous Si half-cells exhibit an excellent cyclability with a high-capacity retention of about 90% at 50 cycles compared to non-porous Si half-cells below 20%. The cross-sectional characteristics of nanoporous and non-porous Si composite anodes are accurately compared using electrochemical impedance spectroscopy and field emission scanning electron microscopy equipped with energy-dispersive X-ray spectroscopy. Based on these results, we conclude that the expansion/contraction of nanosized Si pores and the elastic deformation of Li3PS4 effectively relieve the structural stress derived from the volume change of Si particles/aggregates during lithiation and delithiation, resulting in high cycle stability. These findings provide valuable information for the rational design of Si-based anodes for high-performance ASSLIBs.

Temperature-dependent structural fluctuation and its effect on the electronic structure and charge transport in hybrid perovskite CH3 NH3 PbI3.

The recently discovered hybrid organic-inorganic perovskites have been suggested for high-performance optoelectronic applications. Owing to the mechanical flexibility of these compounds, they demonstrate structural fluctuation at finite temperatures that have been widely discussed with respect to their optical properties. However, the effect of temperature-induced structural fluctuation is not clear until now, with respect to the equally important charge transport properties. In the present study, through ab initio molecular dynamics simulations of cubic-phase CH3 NH3 PbI3 at different temperatures, the temperature-dependent electronic structure and charge carrier transport properties are examined. Compared with the significant structural fluctuation of organic cations, the structural change of the inorganic framework is minor. In addition, because the band edge states at R point are mainly influenced by the anti-bonding character of the Pb-I bond, CH3 NH3 PbI3 demonstrates relatively small deformation potentials as well as low temperature dependence of band gaps (ΔEg ≈ 50 meV from 330 K to 400 K) and electron-phonon coupling strengths, despite the large structural fluctuation of organic cations. Furthermore, the effective mass of the valence band increases with the increase of temperature. The predicted mobilities of CH3 NH3 PbI3 can reach above 75 cm2 V-1 s-1 near room temperature, exhibiting an appropriate optoelectronic potential, while the temperature dependence is steeper than T-1.5 of the traditional semiconductors because of the enhanced effective masses.

X-Ray Tomography Investigation of Cyclically Sheared Granular Materials.

We perform combined x-ray tomography and shear force measurements on a cyclically sheared granular system with highly transient behaviors, and obtain the evolution of microscopic structures and macroscopic shear force during the shear cycle. We explain the macroscopic behaviors of the system based on microscopic processes, including particle level structural rearrangement and frictional contact variation. Specifically, we show how contact friction can induce large structural fluctuations and cause significant shear dilatancy effect for granular materials, and we also construct an empirical constitutive relationship for the macroscopic shear force.

Stable Cyclability Caused by Highly Dispersed Nanoporous Si Composite Anodes with Sulfide-based Solid Electrolyte

All-solid-state lithium-ion batteries (ASSLIBs) without organic liquid electrolytes have attracted considerable attention as a solution to existing safety issues. Si is the most promising anode active material for increasing the energy density of such batteries owing to its high theoretical capacity. However, the stress relaxation of Si with large structural fluctuations is a major challenge to its practical use. In the present study, nanoporous Si particles and a sulfide-based solid electrolyte are composited to accommodate the volumetric expansion. To the best of our knowledge, this is a novel approach in the case of ASSLIBs. We find that the capacity retention of highly dispersed Si composite anodes is 80% up to 150 cycles. Such excellent cyclability is explained by our results, which suggest the following microstructural behavior. The pores in the Si particles act as buffer regions for large volume changes. In addition, the strains arising from the slightly expanded Si particles are relieved by the elasticity of the surrounding sulfide-based solid electrolyte. In summary, this study is a significant step toward the development of high-performance ASSLIBs for various applications.

The gut microbiome in pediatric patients undergoing allogeneic hematopoietic stem cell transplantation.

The gut microbiome (GM) has been associated with different clinical outcomes in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Large multicenter cohort studies in adults have found significant correlations with overall survival, relapse, and incidence of complications. Moreover, GM is already a promising target for therapeutic interventions. However, few data are available in children, a population presenting unique features and challenges. During childhood, the GM evolves rapidly with large structural fluctuations, alongside with the maturation of the immune system. Furthermore, the HSCT procedure presents significant differences in children. These considerations underline the importance of a specific focus on the pediatric setting, and the role of GM and its age-dependent trajectory in influencing the immunity reconstitution and clinical outcomes. This review provides a comprehensive overview of the available evidence in the field of GM and pediatric HSCT, highlighting age-specific issues and discussing GM-based therapeutic approaches.

Efficient Multiexciton State Generation in Charge-Transfer-Coupled Perylene Bisimide Dimers via Structural Control.

The singlet fission (SF) process is generally defined as the conversion of one singlet exciton (S1) into two triplet excitons (2·T1), which has the potential to overcome thermalization losses in the field of photovoltaic devices. Among the applicable compounds for SF-based photovoltaic devices, perylene bisimide (PBI) is one of the best candidates because of its electronic tunability and photostability. However, the strategy for efficient SF in PBIs remains ambiguous because of numerous competing relaxation pathways in PBI-based molecular materials. In this regard, for the first time, we observed the SF mechanism in PBI dimers by controlling the intrinsic factor (exciton coupling) and the external environment (solvent polarity and viscosity). Time-resolved spectroscopic measurements and quantum chemical simulations reveal that efficient SF occurs through the charge-transfer-assisted mechanism, entailing a large structural fluctuation. Our findings not only highlight the SF mechanism in PBI dimers but also suggest the factors responsible for an efficient SF process, which are important considerations in the design of molecular materials for photovoltaic devices.

Critical phenomena in the temperature-pressure-crowding phase diagram of a protein.

In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to maintain structural integrity. These apparently conflicting behaviors are exhibited by systems near a critical point, where distinct phases merge-a concept beyond previous studies indicating proteins have a well-defined folded/unfolded phase boundary in the pressure-temperature plane. Here, by modeling the protein phosphoglycerate kinase (PGK) on the temperature (T), pressure (P), and crowding volume-fraction (ϕ) phase diagram, we demonstrate a critical transition where phases merge, and PGK exhibits large structural fluctuations. Above the critical point, the difference between the intermediate and unfolded phases disappears. When ϕ increases, the critical point moves to lower T c. We verify the calculations with experiments mapping the T-P-ϕ space, which likewise reveal a critical point at 305 K and 170 MPa that moves to lower T c as ϕ increases. Crowding places PGK near a critical line in its natural parameter space, where large conformational changes can occur without costly free energy barriers. Specific structures are proposed for each phase based on simulation.

Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway.

A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.

Coordination to lanthanide ions distorts binding site conformation in calmodulin

The Ca2+-sensing protein calmodulin (CaM) is a popular model of biological ion binding since it is both experimentally tractable and essential to survival in all eukaryotic cells. CaM modulates hundreds of target proteins and is sensitive to complex patterns of Ca2+ exposure, indicating that it functions as a sophisticated dynamic transducer rather than a simple on/off switch. Many details of this transduction function are not well understood. Fourier transform infrared (FTIR) spectroscopy, ultrafast 2D infrared (2D IR) spectroscopy, and electronic structure calculations were used to probe interactions between bound metal ions (Ca2+ and several trivalent lanthanide ions) and the carboxylate groups in CaM's EF-hand ion-coordinating sites. Since Tb3+ is commonly used as a luminescent Ca2+ analog in studies of protein-ion binding, it is important to characterize distinctions between the coordination of Ca2+ and the lanthanides in CaM. Although functional assays indicate that Tb3+ fully activates many Ca2+-dependent proteins, our FTIR spectra indicate that Tb3+, La3+, and Lu3+ disrupt the bidentate coordination geometry characteristic of the CaM binding sites' strongly conserved position 12 glutamate residue. The 2D IR spectra indicate that, relative to the Ca2+-bound form, lanthanide-bound CaM exhibits greater conformational flexibility and larger structural fluctuations within its binding sites. Time-dependent 2D IR lineshapes indicate that binding sites in Ca2+-CaM occupy well-defined configurations, whereas binding sites in lanthanide-bound-CaM are more disordered. Overall, the results show that binding to lanthanide ions significantly alters the conformation and dynamics of CaM's binding sites.

Structure and hydrogen bonds of cyclohexapeptide RA-VII by molecular dynamics simulations and quantum chemical calculations

We computationally examined the structure of anti-tumour bicyclic hexapeptide RA-VII. This peptide adopts three conformations (confs.), A, B and C, in dimethyl sulfoxide (DMSO). Although it was experimentally reported that the structure of conf. A is important for anti-tumour activity, the dynamics of confs. A, B and C are not well known. We performed quantum chemical calculations and molecular dynamics (MD) simulations of RA-VII in DMSO. The MD simulations indicated two different local stable structures for conf. C: a structure containing a bent 18-membered ring and another structure containing a rotated peptide bond between Tyr6 and d-Ala1. The root-mean-square fluctuation of the 14-membered ring for conf. A was larger than that for confs. B and C. Ala4 formed intramolecular hydrogen bonds more often in conf. A than in the other conformations. A large number of hydrogen bonds and large structural fluctuations are important for the anti-tumour activity of RA-VII. Our results for the structural change of conf. C and the analysis of the dynamics for confs. A, B and C may contribute to the design of new analogues of cyclic peptides.

Studying the adsorption of DNA nanostructures on graphene in the aqueous phase using molecular dynamic simulations

DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene. The interaction analyses and energetic calculations show that π-π interactions between single-stranded DNA and graphene are necessary for adsorption of the DNA nanostructures. Overall, this work examined the interactions between DNA and graphene at a large spatial scale with the hope that it provides a new strategy to stabilize DNA nanostructures.

Complex structure of cytochrome c-cytochrome coxidase reveals a novel protein-protein interaction mode.

Mitochondrial cytochrome c oxidase (CcO) transfers electrons from cytochrome c (Cyt.c) to O2 to generate H2O, a process coupled to proton pumping. To elucidate the mechanism of electron transfer, we determined the structure of the mammalian Cyt.c–CcO complex at 2.0‐Å resolution and identified an electron transfer pathway from Cyt.c to CcO. The specific interaction between Cyt.c and CcO is stabilized by a few electrostatic interactions between side chains within a small contact surface area. Between the two proteins are three water layers with a long inter‐molecular span, one of which lies between the other two layers without significant direct interaction with either protein. Cyt.c undergoes large structural fluctuations, using the interacting regions with CcO as a fulcrum. These features of the protein–protein interaction at the docking interface represent the first known example of a new class of protein–protein interaction, which we term “soft and specific”. This interaction is likely to contribute to the rapid association/dissociation of the Cyt.c–CcO complex, which facilitates the sequential supply of four electrons for the O2 reduction reaction.

Oscillatory Enzyme Dynamics Revealed by Two-Dimensional Infrared Spectroscopy.

Enzymes move on a variety of length and time scales. While much is known about large structural fluctuations that impact binding of the substrates and release of products, little is known about faster motions of enzymes and how these motions may influence enzyme-catalyzed reactions. This Letter reports frequency fluctuations of the azide anion bound to the active site of formate dehydrogenase measured via 2D IR spectroscopy. These measurements reveal an underdamped oscillatory component to the frequency-frequency correlation function when the azide is bound to the NAD(+) ternary complex. This oscillation disappears when the reduced cofactor is added, indicating that the oscillating contributions most likely come from the charged nicotinamide ring. These oscillatory motions may be relevant to donor-acceptor distance sampling of the catalyzed hydride transfer and therefore may give future insights into the dynamic behavior involved in enzyme catalysis.

Allosterically Regulated Structural Fluctuation and Microtubule-Binding Affinity of KiF1A -- A Simulation Study of Coarse-Grained Model --

Kinesins are a family of molecular motor proteins that exhibit unidirectional processive motion along the microtubules using the free energy released during the ATP hydrolysis cycle. Kinesin switches its microtuble (MT) binding affinity between strong binding mode and weak binding mode depending on nucleotide states.The allosteric regulation mechanism for this switching, however, is yet to be determined. For understanding this mechanism, we focus on the single-headed kinesin called KIF1A and studied the structural fluctuations of its motor head in different nucleotide states using computer simulations.We constructed a coarse-grained Go-like model for each nucleotide state based on the X-ray structure of KIF1A that binds the corresponding nucleotide analog. Langevin dynamics simulations were used to investigate the structural fluctuations when MT is absent. We found that the helix alpha-4 at the MT binding site intermittently exhibits abrupt large structural fluctuations, actually partial unfolding and folding, which we call as “burst”. Frequency of the burst varies systematically according to the nucleotide states and correlates strongly with the experimentally observed binding affinity to MT. Namely, the binding site becomes more flexible in the strong binding state than in the weak binding state in the absence of MT.Based on this simulation result, we propose the following mechanism for the MT affinity regulation of KIF1A: (1) the flexibility of the MT binding site (helix alpha-4 in particular) is allosterically controlled according to the nucleotide states during the ATP hydrolysis process, (2) the affinity to MT is regulated through the flexibility of the MT binding site, and (3) the more flexible the MT biniding site is, the stronger the binding affinity becomes.

Nucleotide-dependent structural fluctuations and regulation of microtubule-binding affinity of KIF1A.

Molecular motors such as kinesin regulate affinity to a rail protein during the ATP hydrolysis cycle. The regulation mechanism, however, is yet to be determined. To understand this mechanism, we investigated the structural fluctuations of the motor head of the single-headed kinesin called KIF1A in different nucleotide states using molecular dynamics simulations of a Gō-like model. We found that the helix α4 at the microtubule (MT) binding site intermittently exhibits a large structural fluctuation when MT is absent. Frequency of this fluctuation changes systematically according to the nucleotide states and correlates strongly with the experimentally observed binding affinity to MT. We also showed that thermal fluctuation enhances the correlation and the interaction with the nucleotide suppresses the fluctuation of the helix α4. These results suggest that KIF1A regulates affinity to MT by changing the flexibility of the helix α4 during the ATP hydrolysis process: the binding site becomes more flexible in the strong binding state than in the weak binding state.

Conformational frustration in calmodulin-target recognition.

Calmodulin (CaM) is a primary calcium (Ca(2+) )-signaling protein that specifically recognizes and activates highly diverse target proteins. We explored the molecular basis of target recognition of CaM with peptides representing the CaM-binding domains from two Ca(2+) -CaM-dependent kinases, CaMKI and CaMKII, by employing experimentally constrained molecular simulations. Detailed binding route analysis revealed that the two CaM target peptides, although similar in length and net charge, follow distinct routes that lead to a higher binding frustration in the CaM-CaMKII complex than in the CaM-CaMKI complex. We discovered that the molecular origin of the binding frustration is caused by intermolecular contacts formed with the C-domain of CaM that need to be broken before the formation of intermolecular contacts with the N-domain of CaM. We argue that the binding frustration is important for determining the kinetics of the recognition process of proteins involving large structural fluctuations.

Decrypting the Structural, Dynamic and Energetic Basis of Kinesin Interacting with Tubulin Dimer in Three ATPase States by All-Atom Molecular Dynamics Simulation

We have employed molecular dynamics (MD) simulation to investigate, with atomic details, the structural dynamics and energetics of three major ATPase states (ADP, APO and ATP state) of a human kinesin 1 complexed with a tubulin dimer. Starting from a recently solved crystal structure of ATP-like kinesin-tubulin complex by Knossow lab, we have performed flexible fitting of cryo-electron-microscopy maps of kinesin-decorated microtubules, followed with extensive MD simulation (400ns for each state), which is to our knowledge the longest MD simulation of kinesin-tubulin complex published to date. Our modeling and simulation have revealed extensive conformational changes at the tubulin-binding site and the nucleotide-binding pocket of kinesin between ADP, APO and ATP state, featuring a more twisted central β-sheet and a highly flexible and open switch I in APO state. We have found kinesin undergoing large structural fluctuations in APO state toward the direction of ATP state, which allosterically couple nucleotide-binding pocket with tubulin-binding site. We have identified a dynamic network of hydrogen bonds spanning the nucleotide-binding pocket and the kinesin-tubulin binding interface, which are predicted to control and couple nucleotide and tubulin binding during kinesin's ATPase cycle. In addition, we have employed binding free energy analysis to identify a set of key residues involved in kinesin-tubulin binding. Our simulation has also shed light on several outstanding issues in kinesin literature (such as the role of neck linker docking in regulating nucleotide binding, and possible extension/shortening of α4 helix during the ATPase cycle). This study has provided a most comprehensive structural and dynamic picture of kinesin's major ATPase states, and offered promising targets for future mutational and functional studies to investigate the molecular mechanism of kinesin motors.

Structural changes and microstructures in stuffed tridymite-type compounds Ba1−xSrxAl2O4

Crystal structures and microstructures in Ba1−xSrxAl2O4 solid solutions between the end members of BaAl2O4 and SrAl2O4 have been carefully investigated by powder X-ray diffraction, electron diffraction and transmission electron microscopy (TEM) imaging experiments. With the help of fast Fourier transform (FFT) calculation, high-resolution TEM images suggested that diffuse streaks along three equivalent 〈110〉 directions in the (001) plane, which appear in the P63 structure of Ba1−xSrxAl2O4 for x = 0.4, originate from the large structural fluctuation of the AlO4 tetrahedral network. On the other hand, the monoclinic P21 structure in Ba1−xSrxAl2O4 with x = 0.7 was found to consist of a modulated structure with . The present experimental results reveal that a structural phase boundary exists at approximately x = 0.6 between the P63 structure with a large structural fluctuation and a monoclinic P21 phase with the single-q modulated structure.