ABSTRACT
We reconstruct the cosmological background evolution under the scenario of dynamical dark energy through the Gaussian process approach, using the latest Dark Energy Spectroscopic Instrument (DESI) baryon acoustic oscillations (BAO) combined with other observations. Our results reveal that the reconstructed dark-energy equation-of-state (EoS) parameter w(z) exhibits the so-called quintom-B behavior, crossing -1 from phantom to quintessence regime as the universe expands. We investigate under what situation this type of evolution could be achieved from the perspectives of field theories and modified gravity. In particular, we reconstruct the corresponding actions for f(R),f(T), and f(Q) gravity, respectively. We explicitly show that, certain modified gravity can exhibit the quintom dynamics and fit the recent DESI data efficiently, and for all cases the quadratic deviation from the ΛCDM scenario is mildly favored.
ABSTRACT
Molecular aggregation is a powerful tool for tuning advanced materials' photophysical and electronic properties. Here we present a novel potential for the aqueous-solvated aggregated state of boron dipyrromethene (BODIPY) to facilitate phototransformations otherwise achievable only under harsh chemical conditions. We show that the photoinduced symmetry-breaking charge separation state can itself initiate catalyst-free redox chemistry, leading to selective α-C(sp3)-H bond activation/Csp3-Csp3 coupling on the BODIPY backbone. The photoproduction progress was tracked by monitoring the evolution of the strong Stokes-shifted near-infrared emission, resulting from selective self-assembly of the terminal heterodimeric photoproduct into well-ordered J-aggregates, as revealed by X-ray structural analysis. These findings provide a facile and green route to further explore the promising frontier of packing-triggered selective photoconversions via supramolecular engineering.
ABSTRACT
The Hofmeister series is a series of ions ordered according to their ability to precipitate proteins. It has also been linked to a host of (bio)chemical phenomena. Several attempts over the years to correlate the series to the varying success of different salts in crystallising proteins have been largely inconclusive. A correlation, based on published data and crystallisation conditions for several proteins, is proposed here between some thermodynamic properties of proteins and the position in the Hofmeister series of the salts from which they preferentially crystallise. Namely, a high ratio between the entropic or enthalpic protein-solvent interactions contribution to thermodynamic stability and the total thermodynamic stability of a given protein, indicate the protein's high propensity to crystallise in solutions of highly kosmotropic salts. Low such ratios on the other hand, indicate that chaotropic salts can be equally successful, i. e. that the protein in question is rather indifferent to the Hofmeister character of the salt. Testing various model proteins for crystallisation against screens containing salts found at different points on the Hofmeister series, as well as further bibliographic analysis, have yielded results that appear to largely corroborate this hypothesis. These conclusions may conceivably be used as a crystallisation predictive tool.
Subject(s)
Crystallization , Proteins , Salts , Thermodynamics , Proteins/chemistry , Salts/chemistryABSTRACT
Currently, X-ray crystallography, which typically uses synchrotron sources, remains the dominant method for structural determination of proteins and other biomolecules. However, small protein crystals do not provide sufficiently high-resolution diffraction patterns and suffer radiation damage; therefore, conventional X-ray crystallography needs larger protein crystals. The burgeoning method of serial crystallography using X-ray free-electron lasers (XFELs) avoids these challenges: it affords excellent structural data from weakly diffracting objects, including tiny crystals. An XFEL is implemented by irradiating microjets of suspensions of microcrystals with very intense X-ray beams. However, while the method for creating microcrystalline microjets is well established, little attention is given to the growth of high-quality nano/microcrystals suitable for XFEL experiments. In this study, in order to assist the growth of such crystals, we calculate the mean crystal size and the time needed to grow crystals to the desired size in batch crystallization (the predominant method for preparing the required microcrystalline slurries); this time is reckoned theoretically both for microcrystals and for crystals larger than the upper limit of the Gibbs-Thomson effect. The impact of the omnipresent impurities on the growth of microcrystals is also considered quantitatively. Experiments, performed with the model protein lysozyme, support the theoretical predictions.
Subject(s)
Electrons , Synchrotrons , X-Rays , Crystallography, X-Ray , Proteins , LasersABSTRACT
Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass ("Naomi's Nucleant"), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.
Subject(s)
Proteins , Silicon , Crystallization/methods , Crystallography, X-Ray , Gold , Porosity , Proteins/chemistry , Silicon/chemistry , X-Ray DiffractionABSTRACT
Octakis-6-guadinidino-γ-cyclodextrin (gguan) hydrochloride in the presence of phosphates crystallises from aqueous solution in the unprecedented form of a superdimer (dimer-within-a-dimer). The self-assembly exposes four circular octa-guanidinium regions that bind and stabilise discrete H-bonded phosphate anion dimers. The small (â¼2 nm) gguan-phosphate assembly is preorganised and stable in aqueous solution, as demonstrated by DLS and NMR experiments.
Subject(s)
Phosphates , Water , Anions , Hydrogen Bonding , Phosphates/chemistry , Static Electricity , Water/chemistryABSTRACT
The bacterial Rho factor is a ring-shaped motor triggering genome-wide transcription termination and R-loop dissociation. Rho is essential in many species, including in Mycobacterium tuberculosis where rho gene inactivation leads to rapid death. Yet, the M. tuberculosis Rho [MtbRho] factor displays poor NTPase and helicase activities, and resistance to the natural Rho inhibitor bicyclomycin [BCM] that remain unexplained. To address these issues, we solved the cryo-EM structure of MtbRho at 3.3 Šresolution. The MtbRho hexamer is poised into a pre-catalytic, open-ring state wherein specific contacts stabilize ATP in intersubunit ATPase pockets, thereby explaining the cofactor preference of MtbRho. We reveal a leucine-to-methionine substitution that creates a steric bulk in BCM binding cavities near the positions of ATP γ-phosphates, and confers resistance to BCM at the expense of motor efficiency. Our work contributes to explain the unusual features of MtbRho and provides a framework for future antibiotic development.
Subject(s)
Mycobacterium tuberculosis , Bridged Bicyclo Compounds, Heterocyclic , Cryoelectron Microscopy , Mycobacterium tuberculosis/genetics , Mycobacterium tuberculosis/metabolism , Rho Factor/chemistry , Rho Factor/genetics , Rho Factor/metabolism , Transcription Factors/metabolismABSTRACT
Supramolecular organization and self-assembly are the pillars of functionality of many nanosystems. The covalent conjugate (6-spirolactam rhodamine B-6-monodeoxy)-ß-cyclodextrin (Rho-ßCD) is assembled as a self-included, rigid nanostructure, identical in the crystal and in aqueous solution, as revealed by detailed X-ray and NMR analyses. Rho-ßCD self-assembly is the result of an interesting reaction pathway, which partially de-aggregates Rho and disturbs the zwitterionâspirolactone equilibrium. Rho-ßCD is stable at pHâ 4.6, but displays controllable photoswitching between the colored, fluorescent, zwitterionic and the colorless, non-fluorescent closed structures, during several iterative cycles. After an initial drop in absorbance, the on-off process continues without further changes under our irradiation conditions, a consequence of the specific self-locked arrangement of Rho in the cavity. Rho-ßCD exemplifies a water soluble photoresponsive nanosystem with improved photostability suggesting promising applications in super resolution bioimaging.
Subject(s)
beta-Cyclodextrins , Magnetic Resonance Spectroscopy , Rhodamines , WaterABSTRACT
The question of whether "genetic information" is a merely causal factor in development or can be made sense of semantically, in a way analogous to a language or other type of representation, has generated a long debate in the philosophy of biology. It is intimately connected with another intense debate, concerning the limits of genetic determinism. In this paper I argue that widespread attempts to draw analogies between genetic information and information contained in books, blueprints or computer programs, are fundamentally inadequate. In development, gene exons are the central part of an intricate and densely ramified semantic Genetic Informational Network. DNA in the entire genome is in a state of continuous positive and negative feedback with itself and with its 'environment', and is 'read' and acted upon by the cell in various alternative and complementary ways. The linear combinatorial coding relation between codons and amino acids is but one aspect of semantic genetic information, which is, when considered in its entirety, a far wider and richer concept.
Subject(s)
Language , Semantics , DNA , PhilosophyABSTRACT
C-C chemokine receptor 5 (CCR5) is a major co-receptor molecule used by HIV-1 to enter cells. This led to the hypothesis that stimulating an antibody response would block HIV with minimal toxicity. Here, X-ray crystallographic studies of the anti-CCR5 antibody RoAb13 together with two peptides were undertaken: one peptide is a 31-residue peptide containing the PIYDIN sequence and the other is the PIDYIN peptide alone, where PIYDIN is part of the N-terminal region of CCR5 previously shown to be important for HIV entry. In the presence of the longer peptide (the complete N-terminal domain), difference electron density was observed at a site within a hypervariable CDR3 binding region. In the presence of the shorter core peptide PIYDIN, difference electron density is again observed at this CDR3 site, confirming consistent binding for both peptides. This may be useful in the design of a new biomimetic to stimulate an antibody response to CCR5 in order to block HIV infection.
ABSTRACT
Thermofluor or thermal shift assay is an easily implementable, high-throughput method for assessing the thermostability of proteins and the influence of various ligands on that stability. It is particularly useful for the assaying of ligands that may stabilize oligomeric helicases, which rely on both substrates (oligonucleotides) and nucleotide cofactors (ATP analogues) for their stability in a functional state. In this chapter, we describe the rationale and present a basic protocol for the use of this technique. Multi-ligand screening is also discussed via a worked example of the stabilization of a hexameric RNA helicase, a target protein for structural studies in our laboratories.
Subject(s)
Bacterial Proteins/chemistry , Fluorometry/methods , RNA Helicases/chemistry , Rho Factor/chemistry , Mycobacterium tuberculosis/enzymology , Protein Stability , TemperatureABSTRACT
Insulin-regulated aminopeptidase (IRAP) is a transmembrane zinc metallopeptidase with many important biological functions and an emerging pharmacological target. Although previous structural studies have given insight on how IRAP recognizes linear peptides, how it recognizes its physiological cyclic ligands remains elusive. Here, we report the first crystal structure of IRAP with the macrocyclic peptide inhibitor HA08 that combines structural elements from angiotensin IV and the physiological substrates oxytocin and vasopressin. The compound is found in the catalytic site in a near canonical substrate-like configuration and inhibits by a competitive mechanism. Comparison with previously solved structures of IRAP along with small-angle X-ray scattering experiments suggests that IRAP is in an open conformation in solution but undergoes a closing conformational change upon inhibitor binding. Stabilization of the closed conformation in combination with catalytic water exclusion by the tightly juxtaposed GAMEN loop is proposed as a mechanism of inhibition.
ABSTRACT
Local structural frustration, the existence of mutually exclusive competing interactions, may explain why some proteins are dynamic while others are rigid. Frustration is thought to underpin biomolecular recognition and the flexibility of protein-binding sites. Here, we show how a small chemical modification, the oxidation of two cysteine thiols to a disulfide bond, during the catalytic cycle of the N-terminal domain of the key bacterial oxidoreductase DsbD (nDsbD), introduces frustration ultimately influencing protein function. In oxidized nDsbD, local frustration disrupts the packing of the protective cap-loop region against the active site allowing loop opening. By contrast, in reduced nDsbD the cap loop is rigid, always protecting the active-site thiols from the oxidizing environment of the periplasm. Our results point toward an intricate coupling between the dynamics of the active-site cysteines and of the cap loop which modulates the association reactions of nDsbD with its partners resulting in optimized protein function.
Subject(s)
Catalytic Domain , Escherichia coli Proteins/metabolism , Escherichia coli/metabolism , Oxidoreductases/metabolism , Periplasmic Proteins/metabolism , Catalysis , Cysteine/metabolism , Oxidation-Reduction , Periplasm/metabolism , Protein Binding , Sulfhydryl Compounds/metabolismABSTRACT
Macromolecular crystallization is crucial to a large number of scientific fields, including structural biology; drug design, formulation, and delivery; manufacture of biomaterials; and preparation of foodstuffs. The purpose of this study is to facilitate control of crystallization, by investigating hydrophobic interface-assisted protein crystallization both theoretically and experimentally. The application of hydrophobic liquids as nucleation promoters or suppressors has rarely been investigated, and provides an underused avenue to explore in protein crystallization. Theoretically, crystal nucleation is regarded as a two-step process, the first step being a local increase in protein concentration due to its adsorption on the hydrophobic surface. Subsequently, the protein is ordered in a crystal lattice. The energetic aspect of crystal nucleation on water/hydrophobic substance interfaces is approached by calculating the balance between the cohesive energy maintaining integrity of the two-dimensional crystal nucleus and the sum of destructive energies tending to tear up the crystal. This is achieved by comparing the number of bonds shared by the units forming the crystal and the number of unshared (dangling) bonds on the crystal surface pointing toward the solution. The same approach is extended to three-dimensional protein crystal nucleation at water/hydrophobic liquid interfaces. Experimentally, we studied protein crystallization over oils and other hydrophobic liquids (paraffin oil, FC-70 Fluorinert fluorinated oil, and three chlorinated hydrocarbons). Crystallizations of α-lactalbumin and lysozyme are compared, and additional information is acquired by studying α-crustacyanin, trypsin, an insulin analogue, and protein Lpg2936. Depending on the protein type, concentration, and the interface aging time, the proteins exhibit different crystallization propensities depending on the hydrophobic liquid used. Some hydrophobic liquids provoke an increase in the effective supersaturation, which translates to enhancement of crystal nucleation at their interface with the crystallization solution, leading to the formation of crystals.
Subject(s)
Models, Chemical , Oils/chemistry , Paraffin/chemistry , Proteins/chemistry , Crystallization , Crystallography, X-Ray , Hydrophobic and Hydrophilic InteractionsABSTRACT
We construct modified cosmological scenarios through the application of the first law of thermodynamics on the universe horizon, but using the generalized, nonextensive Tsallis entropy instead of the usual Bekenstein-Hawking one. We result to modified cosmological equations that possess the usual ones as a particular limit, but which in the general case contain extra terms that appear for the first time, that constitute an effective dark energy sector quantified by the nonextensive parameter δ . When the matter sector is dust, we extract analytical expressions for the dark energy density and equation-of-state parameters, and we extend these solutions to the case where radiation is present too. We show that the universe exhibits the usual thermal history, with the sequence of matter and dark-energy eras, and according to the value of δ the dark-energy equation-of-state parameter can be quintessence-like, phantom-like, or experience the phantom-divide crossing during the evolution. Even in the case where the explicit cosmological constant is absent, the scenario at hand can very efficiently mimic Λ CDM cosmology, and is in excellent agreement with Supernovae type Ia observational data.
ABSTRACT
Insulin-regulated aminopeptidase (IRAP) is an enzyme with several important biological functions that is known to process a large variety of different peptidic substrates, although the mechanism behind this wide specificity is not clearly understood. We describe a crystal structure of IRAP in complex with a recently developed bioactive and selective inhibitor at 2.53 Å resolution. In the presence of this inhibitor, the enzyme adopts a novel conformation in which domains II and IV are juxtaposed, forming a hollow structure that excludes external solvent access to the catalytic center. A loop adjacent to the enzyme's GAMEN motif undergoes structural reconfiguration, allowing the accommodation of bulky inhibitor side chains. Atomic interactions between the inhibitor and IRAP that are unique to this conformation can explain the strong selectivity compared to homologous aminopeptidases ERAP1 and ERAP2. This conformation provides insight on IRAP's catalytic cycle and reveals significant active-site plasticity that may underlie its substrate permissiveness.
Subject(s)
Cystinyl Aminopeptidase/antagonists & inhibitors , Cystinyl Aminopeptidase/metabolism , Enzyme Inhibitors/pharmacology , Protein Conformation/drug effects , Catalytic Domain/drug effects , Crystallography, X-Ray , Cystinyl Aminopeptidase/chemistry , Enzyme Inhibitors/chemistry , Humans , Ligands , Models, Molecular , Peptides/metabolism , Substrate SpecificityABSTRACT
Endoplasmic reticulum aminopeptidase 2 assists with the generation of antigenic peptides for presentation onto Major Histocompatibility Class I molecules in humans. Recent evidence has suggested that the activity of ERAP2 may contribute to the generation of autoimmunity, thus making ERAP2 a possible pharmacological target for the regulation of adaptive immune responses. To better understand the structural elements of inhibitors that govern their binding affinity to the ERAP2 active site, we cocrystallized ERAP2 with a medium activity 3,4-diaminobenzoic acid inhibitor and a poorly active hydroxamic acid derivative. Comparison of these two crystal structures with a previously solved structure of ERAP2 in complex with a potent phosphinic pseudopeptide inhibitor suggests that engaging the substrate N-terminus recognition properties of the active site is crucial for inhibitor binding even in the absence of a potent zinc-binding group. Proper utilization of all five major pharmacophores is necessary, however, to optimize inhibitor potency.
ABSTRACT
The most powerful method for protein structure determination is X-ray crystallography which relies on the availability of high quality crystals. Obtaining protein crystals is a major bottleneck, and inducing their nucleation is of crucial importance in this field. An effective method to form crystals is to introduce nucleation-inducing heterologous materials into the crystallization solution. Porous materials are exceptionally effective at inducing nucleation. It is shown here that a combined diffusion-adsorption effect can increase protein concentration inside pores, which enables crystal nucleation even under conditions where heterogeneous nucleation on flat surfaces is absent. Provided the pore is sufficiently narrow, protein molecules approach its walls and adsorb more frequently than they can escape. The decrease in the nucleation energy barrier is calculated, exhibiting its quantitative dependence on the confinement space and the energy of interaction with the pore walls. These results provide a detailed explanation of the effectiveness of porous materials for nucleation of protein crystals, and will be useful for optimal design of such materials.
Subject(s)
Crystallization/methods , Proteins/chemistry , Adsorption , Crystallography, X-Ray , Diffusion , Energy Metabolism , Models, Theoretical , PorosityABSTRACT
Over recent decades, the role of torsion in gravity has been extensively investigated along the main direction of bringing gravity closer to its gauge formulation and incorporating spin in a geometric description. Here we review various torsional constructions, from teleparallel, to Einstein-Cartan, and metric-affine gauge theories, resulting in extending torsional gravity in the paradigm of f (T) gravity, where f (T) is an arbitrary function of the torsion scalar. Based on this theory, we further review the corresponding cosmological and astrophysical applications. In particular, we study cosmological solutions arising from f (T) gravity, both at the background and perturbation levels, in different eras along the cosmic expansion. The f (T) gravity construction can provide a theoretical interpretation of the late-time universe acceleration, alternative to a cosmological constant, and it can easily accommodate with the regular thermal expanding history including the radiation and cold dark matter dominated phases. Furthermore, if one traces back to very early times, for a certain class of f (T) models, a sufficiently long period of inflation can be achieved and hence can be investigated by cosmic microwave background observations-or, alternatively, the Big Bang singularity can be avoided at even earlier moments due to the appearance of non-singular bounces. Various observational constraints, especially the bounds coming from the large-scale structure data in the case of f (T) cosmology, as well as the behavior of gravitational waves, are described in detail. Moreover, the spherically symmetric and black hole solutions of the theory are reviewed. Additionally, we discuss various extensions of the f (T) paradigm. Finally, we consider the relation with other modified gravitational theories, such as those based on curvature, like f (R) gravity, trying to illuminate the subject of which formulation, or combination of formulations, might be more suitable for quantization ventures and cosmological applications.
ABSTRACT
X-ray crystallography is the most powerful method for determining three-dimensional structures of proteins to (near-)atomic resolution, but protein crystallization is a poorly explained and often intractable phenomenon. Differential Scanning Calorimetry was used to measure the thermodynamic parameters (ΔG, ΔH, ΔS) of temperature-driven unfolding of two globular proteins, lysozyme, and ribonuclease A, in various salt solutions. The mixtures were categorized into those that were conducive to crystallization of the protein and those that were not. It was found that even fairly low salt concentrations had very large effects on thermodynamic parameters. High concentrations of salts conducive to crystallization stabilized the native folded forms of proteins, whereas high concentrations of salts that did not crystallize them tended to destabilize them. Considering the ΔH and TΔS contributions to the ΔG of unfolding separately, high concentrations of crystallizing salts were found to enthalpically stabilize and entropically destabilize the protein, and vice-versa for the noncrystallizing salts. These observations suggest an explanation, in terms of protein stability and entropy of hydration, of why some salts are good crystallization agents for a given protein and others are not. This in turn provides theoretical insight into the process of protein crystallization, suggesting ways of predicting and controlling it. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 642-652, 2016.