Showing papers in "Protein Science in 2013"

Cool horizons for entangled black holes

Abstract: General relativity contains solutions in which two distant black holes are connected through the interior via a wormhole, or Einstein-Rosen bridge. These solutions can be interpreted as maximally entangled states of two black holes that form a complex EPR pair. We suggest that similar bridges might be present for more general entangled states. In the case of entangled black holes one can formulate versions of the AMPS(S) paradoxes and resolve them. This suggests possible resolutions of the firewall paradoxes for more general situations.

A decade and a half of protein intrinsic disorder: Biology still waits for physics

Abstract: The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of ordered secondary structure, and are characterized by high structural heterogeneity. They are very flexible, but some may undergo disorder to order transitions in the presence of natural ligands. The degree of these structural rearrangements varies over a very wide range. IDPs/IDPRs are tightly controlled under the normal conditions and have numerous specific functions that complement functions of ordered proteins and domains. When lacking proper control, they have multiple roles in pathogenesis of various human diseases. Gaining structural and functional information about these proteins is a challenge, since they do not typically “freeze” while their “pictures are taken.” However, despite or perhaps because of the experimental challenges, these fuzzy objects with fuzzy structures and fuzzy functions are among the most interesting targets for modern protein research. This review briefly summarizes some of the recent advances in this exciting field and considers some of the basic lessons learned from the analysis of physics, chemistry, and biology of IDPs.

Black hole's quantum N-portrait

Abstract: We establish a quantum measure of classicality in the form of the occupation number, N, of gravitons in a gravitational field. This allows us to view classical background geometries as quantum Bose-condensates with large occupation numbers of soft gravitons. We show that among all possible sources of a given physical length, N is maximized by the black hole and coincides with its entropy. The emerging quantum mechanical picture of a black hole is surprisingly simple and fully parameterized by N. The black hole is a leaky bound-state in form of a cold Bose-condensate of N weakly-interacting soft gravitons of wave-length N**(1/2) times the Planck length and of quantum interaction strength 1/N. Such a bound-state exists for an arbitrary N. This picture provides a simple quantum description of the phenomena of Hawking radiation, Bekenstein entropy as well as of non-Wilsonian UV-self-completion of Einstein gravity. We show that Hawking radiation is nothing but a quantum depletion of the graviton Bose-condensate, which despite the zero temperature of the condensate produces a thermal spectrum of temperature T = 1/(N**(1/2)). The Bekenstein entropy originates from the exponentially growing with N number of quantum states. Finally, our quantum picture allows to understand classicalization of deep-UV gravitational scattering as 2 -> N transition. We point out some fundamental similarities between the black holes and solitons, such as a t'Hooft-Polyakov monopole. Both objects represent Bose-condensates of N soft bosons of wavelength N**(1/2) and interaction strength 1/N. In short, the semi-classical black hole physics is 1/N-coupled large-N quantum physics.

Halogen bonding (X‐bonding): A biological perspective

Abstract: The concept of the halogen bond (or X-bond) has become recognized as contributing significantly to the specificity in recognition of a large class of halogenated compounds. The interaction is most easily understood as primarily an electrostatically driven molecular interaction, where an electropositive crown, or σ-hole, serves as a Lewis acid to attract a variety of electron-rich Lewis bases, in analogous fashion to a classic hydrogen bonding (H-bond) interaction. We present here a broad overview of X-bonds from the perspective of a biologist who may not be familiar with this recently rediscovered class of interactions and, consequently, may be interested in how they can be applied as a highly directional and specific component of the molecular toolbox. This overview includes a discussion for where X-bonds are found in biomolecular structures, and how their structure–energy relationships are studied experimentally and modeled computationally. In total, our understanding of these basic concepts will allow X-bonds to be incorporated into strategies for the rational design of new halogenated inhibitors against biomolecular targets or toward molecular engineering of new biological-based materials.

The spacetime of double field theory: Review, remarks, and outlook

Abstract: We review double field theory (DFT) with emphasis on the doubled spacetime and its generalized coordinate transformations, which unify diffeomorphisms and b-field gauge transformations. We illustrate how the composition of generalized coordinate transformations fails to associate. Moreover, in dimensional reduction, the O(d,d) T-duality transformations of fields can be obtained as generalized diffeomorphisms. Restricted to a half-dimensional subspace, DFT includes ‘generalized geometry’, but is more general in that local patches of the doubled space may be glued together with generalized coordinate transformations. Indeed, we show that for certain T-fold backgrounds with nongeometric fluxes, there are generalized coordinate transformations that induce, as gauge symmetries of DFT, the requisite O(d,d;Z) monodromy transformations. Finally we review recent results on the α ′ extension of DFT which, reduced to the half-dimensional subspace, yields intriguing modifications of the basic structures of generalized geometry.

Sequence-specific determination of protein and peptide concentrations by absorbance at 205 nm.

Abstract: Quantitative studies in molecular and structural biology generally require accurate and precise determination of protein concentrations, preferably via a method that is both quick and straightforward to perform. The measurement of ultraviolet absorbance at 280 nm has proven especially useful, since the molar absorptivity (extinction coefficient) at 280 nm can be predicted directly from a protein sequence. This method, however, is only applicable to proteins that contain tryptophan or tyrosine residues. Absorbance at 205 nm, among other wavelengths, has been used as an alternative, although generally using absorptivity values that have to be uniquely calibrated for each protein, or otherwise only roughly estimated. Here, we propose and validate a method for predicting the molar absorptivity of a protein or peptide at 205 nm directly from its amino acid sequence, allowing one to accurately determine the concentrations of proteins that do not contain tyrosine or tryptophan residues. This method is simple to implement, requires no calibration, and should be suitable for a wide range of proteins and peptides.

Linkers in the structural biology of protein–protein interactions

Abstract: Linkers or spacers are short amino acid sequences created in nature to separate multiple domains in a single protein. Most of them are rigid and function to prohibit unwanted interactions between the discrete domains. However, Gly-rich linkers are flexible, connecting various domains in a single protein without interfering with the function of each domain. The advent of recombinant DNA technology made it possible to fuse two interacting partners with the introduction of artificial linkers. Often, independent proteins may not exist as stable or structured proteins until they interact with their binding partner, following which they gain stability and the essential structural elements. Gly-rich linkers have been proven useful for these types of unstable interactions, particularly where the interaction is weak and transient, by creating a covalent link between the proteins to form a stable protein-protein complex. Gly-rich linkers are also employed to form stable covalently linked dimers, and to connect two independent domains that create a ligand-binding site or recognition sequence. The lengths of linkers vary from 2 to 31 amino acids, optimized for each condition so that the linker does not impose any constraints on the conformation or interactions of the linked partners. Various structures of covalently linked protein complexes have been described using X-ray crystallography, nuclear magnetic resonance and cryo-electron microscopy techniques. In this review, we evaluate several structural studies where linkers have been used to improve protein quality, to produce stable protein-protein complexes, and to obtain protein dimers.

Protein–protein interactions: General trends in the relationship between binding affinity and interfacial buried surface area

Abstract: Protein–protein interactions play key roles in many cellular processes and their affinities and specificities are finely tuned to the functions they perform. Here, we present a study on the relationship between binding affinity and the size and chemical nature of protein–protein interfaces. Our analysis focuses on heterodimers and includes curated structural and thermodynamic data for 113 complexes. We observe a direct correlation between binding affinity and the amount of surface area buried at the interface. For a given amount of surface area buried, the binding affinity spans four orders of magnitude in terms of the dissociation constant (Kd). Across the entire dataset, we observe no obvious relationship between binding affinity and the chemical composition of the interface. We also calculate the free energy per unit surface area buried, or “surface energy density,” of each heterodimer. For interfacial surface areas between 500 and 2000 A2, the surface energy density decreases as the buried surface area increases. As the buried surface area increases beyond about 2000 A2, the surface energy density levels off to a constant value. We believe that these analyses and data will be useful for researchers with an interest in understanding, designing or inhibiting protein–protein interfaces.

Molecular basis of MAP kinase regulation

Abstract: Mitogen-activated protein kinases (MAPKs; ERK1/2, p38, JNK, and ERK5) have evolved to transduce environmental and developmental signals (growth factors, stress) into adaptive and programmed responses (differentiation, inflammation, apoptosis). Almost 20 years ago, it was discovered that MAPKs contain a docking site in the C-terminal lobe that binds a conserved 13-16 amino acid sequence known as the D- or KIM-motif (kinase interaction motif). Recent crystal structures of MAPK:KIM-peptide complexes are leading to a precise understanding of how KIM sequences contribute to MAPK selectivity. In addition, new crystal and especially NMR studies are revealing how residues outside the canonical KIM motif interact with specific MAPKs and contribute further to MAPK selectivity and signaling pathway fidelity. In this review, we focus on these recent studies, with an emphasis on the use of NMR spectroscopy, isothermal titration calorimetry and small angle X-ray scattering to investigate these processes.

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding.

Abstract: Molecular recognition features (MoRFs) are intrinsically disordered protein regions that bind to partners via disorder-to-order transitions. In one-to-many binding, a single MoRF binds to two or more different partners individually. MoRF-based one-to-many protein–protein interaction (PPI) examples were collected from the Protein Data Bank, yielding 23 MoRFs bound to 2–9 partners, with all pairs of same-MoRF partners having less than 25% sequence identity. Of these, 8 MoRFs were bound to 2–9 partners having completely different folds, whereas 15 MoRFs were bound to 2–5 partners having the same folds but with low sequence identities. For both types of partner variation, backbone and side chain torsion angle rotations were used to bring about the conformational changes needed to enable close fits between a single MoRF and distinct partners. Alternative splicing events (ASEs) and posttranslational modifications (PTMs) were also found to contribute to distinct partner binding. Because ASEs and PTMs both commonly occur in disordered regions, and because both ASEs and PTMs are often tissue-specific, these data suggest that MoRFs, ASEs, and PTMs may collaborate to alter PPI networks in different cell types. These data enlarge the set of carefully studied MoRFs that use inherent flexibility and that also use ASE-based and/or PTM-based surface modifications to enable the same disordered segment to selectively associate with two or more partners. The small number of residues involved in MoRFs and in their modifications by ASEs or PTMs may simplify the evolvability of signaling network diversity.

Polylogarithms, multiple zeta values and superstring amplitudes

Abstract: A formalism is provided to calculate tree amplitudes in open superstring theory for any multiplicity at any order in the inverse string tension. We point out that the underlying world-sheet disk integrals share substantial properties with color-ordered tree amplitudes in Yang-Mills field theories. In particular, we closely relate world-sheet integrands of open-string tree amplitudes to the Kawai-Lewellen-Tye representation of supergravity amplitudes. This correspondence helps to reduce the singular parts of world-sheet disk integrals – including their string corrections – to lower-point results. The remaining regular parts are systematically addressed by polylogarithm manipulations.

A comparison of successful and failed protein interface designs highlights the challenges of designing buried hydrogen bonds

Abstract: The accurate design of new protein–protein interactions is a longstanding goal of computational protein design. However, most computationally designed interfaces fail to form experimentally. This investigation compares five previously described successful de novo interface designs with 158 failures. Both sets of proteins were designed with the molecular modeling program Rosetta. Designs were considered a success if a high-resolution crystal structure of the complex closely matched the design model and the equilibrium dissociation constant for binding was less than 10 μM. The successes and failures represent a wide variety of interface types and design goals including heterodimers, homodimers, peptide-protein interactions, one-sided designs (i.e., where only one of the proteins was mutated) and two-sided designs. The most striking feature of the successful designs is that they have fewer polar atoms at their interfaces than many of the failed designs. Designs that attempted to create extensive sets of interface-spanning hydrogen bonds resulted in no detectable binding. In contrast, polar atoms make up more than 40% of the interface area of many natural dimers, and native interfaces often contain extensive hydrogen bonding networks. These results suggest that Rosetta may not be accurately balancing hydrogen bonding and electrostatic energies against desolvation penalties and that design processes may not include sufficient sampling to identify side chains in preordered conformations that can fully satisfy the hydrogen bonding potential of the interface.

Tri‐bimaximal neutrino mixing and discrete flavour symmetries

Abstract: We review the application of non-Abelian discrete groups to Tri-Bimaximal (TB) neutrino mixing, which is supported by experiment as a possible good first approximation to the data. After summarizing the motivation and the formalism, we discuss specific models, mainly those based on A_4 but also on other finite groups, and their phenomenological implications, including the extension to quarks. The recent measurements of theta_13 favour versions of these models where a suitable mechanism leads to corrections to theta_13 that can naturally be larger than those to theta_12 and theta_23. The virtues and the problems of TB mixing models are discussed, also in connection with lepton flavour violating processes, and the different approaches are compared.

Evolution of crystallins for a role in the vertebrate eye lens

Abstract: The camera eye lens of vertebrates is a classic example of the re-engineering of existing protein components to fashion a new device. The bulk of the lens is formed from proteins belonging to two superfamilies, the α-crystallins and the βγ-crystallins. Tracing their ancestry may throw light on the origin of the optics of the lens. The α-crystallins belong to the ubiquitous small heat shock proteins family that plays a protective role in cellular homeostasis. They form enormous polydisperse oligomers that challenge modern biophysical methods to uncover the molecular basis of their assembly structure and chaperone-like protein binding function. It is argued that a molecular phenotype of a dynamic assembly suits a chaperone function as well as a structural role in the eye lens where the constraint of preventing protein condensation is paramount. The main cellular partners of α-crystallins, the β- and γ-crystallins, have largely been lost from the animal kingdom but the superfamily is hugely expanded in the vertebrate eye lens. Their structures show how a simple Greek key motif can evolve rapidly to form a complex array of monomers and oligomers. Apart from remaining transparent, a major role of the partnership of α-crystallins with β- and γ-crystallins in the lens is to form a refractive index gradient. Here, we show some of the structural and genetic features of these two protein superfamilies that enable the rapid creation of different assembly states, to match the rapidly changing optical needs among the various vertebrates.

Structure and function of the SPRY/B30.2 domain proteins involved in innate immunity

Abstract: The SPRY domain is a protein interaction module found in 77 murine and ~100 human proteins, and is implicated in important biological pathways, including those that regulate innate and adaptive immunity. The current definition of the SPRY domain is based on a sequence repeat discovered in the splA kinase and ryanodine receptors. The greater SPRY family is divided into the B30.2 (which contains a PRY extension at the N-terminus) and "SPRY-only" sub-families. In this brief review, we examine the current structural and biochemical literature on SPRY/B30.2 domain involvement in key immune processes and highlight a PRY-like 60 amino acid region in the N-terminus of "SPRY-only" proteins. Phylogenetic, structural, and functional analyses suggest that this N-terminal region is related to the PRY region of B30.2 and should be characterized as part of an extended SPRY domain. Greater understanding of the functional importance of the N-terminal region in "SPRY only" proteins will enhance our ability to interrogate SPRY interactions with their respective binding partners.

Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria

Abstract: Bacterial microcompartment (MCP) organelles are cytosolic, polyhedral structures consisting of a thin protein shell and a series of encapsulated, sequentially acting enzymes. To date, different microcompartments carrying out three distinct types of metabolic processes have been characterized experimentally in various bacteria. In the present work, we use comparative genomics to explore the existence of yet uncharacterized microcompartments encapsulating a broader set of metabolic pathways. A clustering approach was used to group together enzymes that show a strong tendency to be encoded in chromosomal proximity to each other while also being near genes for microcompartment shell proteins. The results uncover new types of putative microcompartments, including one that appears to encapsulate B12-independent, glycyl radical-based degradation of 1,2-propanediol, and another potentially involved in amino alcohol metabolism in mycobacteria. Preliminary experiments show that an unusual shell protein encoded within the glycyl radical-based microcompartment binds an iron-sulfur cluster, hinting at complex mechanisms in this uncharacterized system. In addition, an examination of the computed microcompartment clusters suggests the existence of specific functional variations within certain types of MCPs, including the alpha carboxysome and the glycyl radical-based microcompartment. The findings lead to a deeper understanding of bacterial microcompartments and the pathways they sequester.

To fuse or not to fuse: What is your purpose?

Abstract: Since the dawn of time, or at least the dawn of recombinant DNA technology (which for many of today's scientists is the same thing), investigators have been cloning and expressing heterologous proteins in a variety of different cells for a variety of different reasons. These range from cell biological studies looking at protein-protein interactions, post-translational modifications, and regulation, to laboratory-scale production in support of biochemical, biophysical, and structural studies, to large scale production of potential biotherapeutics. In parallel, fusion-tag technology has grown-up to facilitate microscale purification (pull-downs), protein visualization (epitope tags), enhanced expression and solubility (protein partners, e.g., GST, MBP, TRX, and SUMO), and generic purification (e.g., His-tags, streptag, and FLAG™-tag). Frequently, these latter two goals are combined in a single fusion partner. In this review, we examine the most commonly used fusion methodologies from the perspective of the ultimate use of the tagged protein. That is, what are the most commonly used fusion partners for pull-downs, for structural studies, for production of active proteins, or for large-scale purification? What are the advantages and limitations of each? This review is not meant to be exhaustive and the approach undoubtedly reflects the experiences and interests of the authors. For the sake of brevity, we have largely ignored epitope tags although they receive wide use in cell biology for immunopreciptation.

Lipase in aqueous-polar organic solvents: Activity, structure, and stability

Abstract: Studying alterations in biophysical and biochemical behavior of enzymes in the presence of organic solvents and the underlying cause(s) has important implications in biotechnology. We investigated the effects of aqueous solutions of polar organic solvents on ester hydrolytic activity, structure and stability of a lipase. Relative activity of the lipase monotonically decreased with increasing concentration of acetone, acetonitrile, and DMF but increased at lower concentrations (upto ∼20% v/v) of dimethylsulfoxide, isopropanol, and methanol. None of the organic solvents caused any appreciable structural change as evident from circular dichorism and NMR studies, thus do not support any significant role of enzyme denaturation in activity change. Change in 2D [15N, 1H]-HSQC chemical shifts suggested that all the organic solvents preferentially localize to a hydrophobic patch in the active-site vicinity and no chemical shift perturbation was observed for residues present in protein's core. This suggests that activity alteration might be directly linked to change in active site environment only. All organic solvents decreased the apparent binding of substrate to the enzyme (increased Km); however significantly enhanced the kcat. Melting temperature (Tm) of lipase, measured by circular dichroism and differential scanning calorimetry, altered in all solvents, albeit to a variable extent. Interestingly, although the effect of all organic solvents on various properties on lipase is qualitatively similar, our study suggest that magnitudes of effects do not appear to follow bulk solvent properties like polarity and the solvent effects are apparently dictated by specific and local interactions of solvent molecule(s) with the protein.

Nucleophosmin mutations in acute myeloid leukemia: a tale of protein unfolding and mislocalization.

Abstract: Nucleophosmin (NPM1) is an abundant, ubiquitously expressed protein mainly localized at nucleoli but continuously shuttling between nucleus and cytoplasm. NPM1 plays a role in several cellular functions, including ribosome biogenesis and export, centrosome duplication, chromatin remodeling, DNA repair, and response to stress stimuli. Much of the interest in this protein arises from its relevance in human malignancies. NPM1 is frequently overexpressed in solid tumors and is the target of several chromosomal translocations in hematologic neoplasms. Notably, NPM1 has been characterized as the most frequently mutated gene in acute myeloid leukemia (AML). Mutations alter the C-terminal DNA-binding domain of the protein and result in its aberrant nuclear export and stable cytosolic localization. In this review, we focus on the leukemia-associated NPM1 C-terminal domain and describe its structure, function, and the effect exerted by leukemic mutations. Finally, we discuss the possibility to target NPM1 for the treatment of cancer and, in particular, of AML patients with mutated NPM1 gene.

Mass spectrometry‐based methods to study protein architecture and dynamics

Abstract: Mass spectrometry is now an indispensable tool in the armamentarium of molecular biophysics, where it is used for tasks ranging from protein sequencing and mapping of post-translational modifications to studies of higher order structure, conformational dynamics, and interactions of proteins with small molecule ligands and other biopolymers. This mini-review highlights several popular mass spectrometry-based tools that are now commonly used for structural studies of proteins beyond their covalent structure with a particular emphasis on hydrogen exchange and direct electrospray ionization mass spectrometry.

Thermal stability of lysozyme as a function of ion concentration: a reappraisal of the relationship between the Hofmeister series and protein stability.

Abstract: Anion and cation effects on the structural stability of lysozyme were investigated using differential scanning calorimetry. At low concentrations (<5 mM) anions and cations alter the stability of lysozyme but they do not follow the Hofmeister (or inverse Hofmeister) series. At higher concentrations protein stabilization follows the well-established Hofmeister series. Our hypothesis is that there are three mechanisms at work. At low concentrations the anions interact with charged side chains where the presence of the ion can alter the structural stability of the protein. At higher concentrations the low charge density anions perchlorate and iodide interact weakly with the protein. Their presence however reduces the Gibbs free energy required to hydrate the core of the protein that is exposed during unfolding therefore destabilizing the structure. At higher concentrations the high charge density anions phosphate and sulfate compete for water with the protein as it unfolds increasing the Gibbs free energy required to hydrate the newly exposed core of the protein therefore stabilizing the structure.

A common landscape for membrane-active peptides.

Abstract: Three families of membrane-active peptides are commonly found in nature and are classified according to their initial apparent activity. Antimicrobial peptides are ancient components of the innate immune system and typically act by disruption of microbial membranes leading to cell death. Amyloid peptides contribute to the pathology of diverse diseases from Alzheimer's to type II diabetes. Preamyloid states of these peptides can act as toxins by binding to and permeabilizing cellular membranes. Cell-penetrating peptides are natural or engineered short sequences that can spontaneously translocate across a membrane. Despite these differences in classification, many similarities in sequence, structure, and activity suggest that peptides from all three classes act through a small, common set of physical principles. Namely, these peptides alter the Brownian properties of phospholipid bilayers, enhancing the sampling of intrinsic fluctuations that include membrane defects. A complete energy landscape for such systems can be described by the innate membrane properties, differential partition, and the associated kinetics of peptides dividing between surface and defect regions of the bilayer. The goal of this review is to argue that the activities of these membrane-active families of peptides simply represent different facets of what is a shared energy landscape.

A flexible docking approach for prediction of T cell receptor–peptide–MHC complexes

Abstract: T cell receptors (TCRs) are immune proteins that specifically bind to antigenic molecules, which are often foreign peptides presented by major histocompatibility complex proteins (pMHCs), playing a key role in the cellular immune response. To advance our understanding and modeling of this dynamic immunological event, we assembled a protein-protein docking benchmark consisting of 20 structures of crystallized TCR/pMHC complexes for which unbound structures exist for both TCR and pMHC. We used our benchmark to compare predictive performance using several flexible and rigid backbone TCR/pMHC docking protocols. Our flexible TCR docking algorithm, TCRFlexDock, improved predictive success over the fixed backbone protocol, leading to near-native predictions for 80% of the TCR/pMHC cases among the top 10 models, and 100% of the cases in the top 30 models. We then applied TCRFlexDock to predict the two distinct docking modes recently described for a single TCR bound to two different antigens, and tested several protein modeling scoring functions for prediction of TCR/pMHC binding affinities. This algorithm and benchmark should enable future efforts to predict, and design of uncharacterized TCR/pMHC complexes.

Cryo-EM model validation using independent map reconstructions.

Abstract: An increasing number of cryo-electron microscopy (cryo-EM) density maps are being generated with suitable resolution to trace the protein backbone and guide sidechain placement. Generating and evaluating atomic models based on such maps would be greatly facilitated by independent validation metrics for assessing the fit of the models to the data. We describe such a metric based on the fit of atomic models with independent test maps from single particle reconstructions not used in model refinement. The metric provides a means to determine the proper balance between the fit to the density and model energy and stereochemistry during refinement, and is likely to be useful in determining values of model building and refinement metaparameters quite generally.

Bacterial microcompartment shells of diverse functional types possess pentameric vertex proteins.

Abstract: Bacterial microcompartments (MCPs) are large proteinaceous structures comprised of a roughly icosahedral shell and a series of encapsulated enzymes. MCPs carrying out three different metabolic functions have been characterized in some detail, while gene expression and bioinformatics studies have implicated other types, including one believed to perform glycyl radical-based metabolism of 1,2-propanediol (Grp). Here we report the crystal structure of a protein (GrpN), which is presumed to be part of the shell of a Grp-type MCP in Rhodospirillum rubrum F11. GrpN is homologous to a family of proteins (EutN/PduN/CcmL/CsoS4) whose members have been implicated in forming the vertices of MCP shells. Consistent with that notion, the crystal structure of GrpN revealed a pentameric assembly. That observation revived an outstanding question about the oligomeric state of this protein family: pentameric forms (for CcmL and CsoS4A) and a hexameric form (for EutN) had both been observed in previous crystal structures. To clarify these confounding observations, we revisited the case of EutN. We developed a molecular biology-based method for accurately determining the number of subunits in homo-oligomeric proteins, and found unequivocally that EutN is a pentamer in solution. Based on these convergent findings, we propose the name bacterial microcompartment vertex for this special family of MCP shell proteins.

Entanglement of identical particles and the detection process

Abstract: We introduce detector-level entanglement, a unified entanglement concept for identical particles that takes into account the possible deletion of many-particle which-way information through the detection process. The concept implies a measure for the effective indistinguishability of the particles, which is controlled by the measurement setup and which quantifies the extent to which the (anti-)symmetrization of the wave-function impacts on physical observables. Initially indistinguishable particles can gain or loose entanglement on their transition to distinguishability, and their quantum statistical behavior depends on their initial entanglement. Our results show that entanglement cannot be attributed to a state of identical particles alone, but that the detection process has to be incorporated in the analysis.

The S3 flavour symmetry: Neutrino masses and mixings

Abstract: In this work, we discuss the neutrino masses and mixings as the realization of an S3 flavour permutational symmetry in two models, namely the Standard Model and an extension of the Standard Model with three Higgs doublets. In the S3 Standard Model, mass matrices of the same generic form are obtained for the neutrino and charged leptons when the S3 flavour symmetry is broken sequentially according to the chain S3L ⊗ S3R ⊃ S3diag ⊃ S2. In the minimal S3-symmetric extension of the Standard Model, the S3 symmetry is left unbroken, and the concept of flavour is extended to the Higgs sector by introducing in the theory three Higgs fields which are SU(2) doublets. In both models, the mass matrices of the neutrinos and charged leptons are reparametrized in terms of their eigenvalues, and exact, explicit analytical expressions for the neutrino mixing angles as functions of the masses of neutrinos and charged leptons are obtained. In the case of the S3 Standard Model, from a χ2 fit of the theoretical expressions of the lepton mixing matrix to the values extracted from experiment, the numerical values of the neutrino mixing angles are obtained in excellent agreement with experimental data. In the S3 extension of the Standard Model, if two of the right handed neutrinos masses are degenerate, the reactor and atmospheric mixing angles are determined by the masses of the charged leptons, yielding θ23 in excellent agreement with experimental data, and θ13 different from zero but very small. If the masses of the three right handed neutrinos are assumed to be different, then it is possible to get θ13also in very good agreement with experimental data. We also show the branching ratios of some selected flavour changing neutral currents (FCNC) process as well as the contribution of the exchange of a neutral flavour changing scalar to the anomaly of the magnetic moment of the muon.

Status of three-neutrino oscillation parameters

Abstract: Here we review the current status of global fits to neutrino oscillation data within the three-flavour framework. In our analysis we include the most recent data from solar and atmospheric neutrino experiments as well as the latest results from the long-baseline accelerator neutrino experiments and the recent measurements of reactor neutrino disappearance reported by Double Chooz, Daya Bay and RENO. We present updated determinations for the two neutrino mass splittings and the three mixing angles responsible for neutrino oscillations that, for the first time, have all been measured with 1σ accuracies ranging from 3 to 15%. A weak sensitivity for the CP violating phase δ is also reported from the global analysis.

Insulin analog with additional disulfide bond has increased stability and preserved activity.

Abstract: Insulin is a key hormone controlling glucose homeostasis. All known vertebrate insulin analogs have a classical structure with three 100% conserved disulfide bonds that are essential for structural stability and thus the function of insulin. It might be hypothesized that an additional disulfide bond may enhance insulin structural stability which would be highly desirable in a pharmaceutical use. To address this hypothesis, we designed insulin with an additional interchain disulfide bond in positions A10/B4 based on Cα-Cα distances, solvent exposure, and side-chain orientation in human insulin (HI) structure. This insulin analog had increased affinity for the insulin receptor and apparently augmented glucodynamic potency in a normal rat model compared with HI. Addition of the disulfide bond also resulted in a 34.6°C increase in melting temperature and prevented insulin fibril formation under high physical stress even though the C-terminus of the B-chain thought to be directly involved in fibril formation was not modified. Importantly, this analog was capable of forming hexamer upon Zn addition as typical for wild-type insulin and its crystal structure showed only minor deviations from the classical insulin structure. Furthermore, the additional disulfide bond prevented this insulin analog from adopting the R-state conformation and thus showing that the R-state conformation is not a prerequisite for binding to insulin receptor as previously suggested. In summary, this is the first example of an insulin analog featuring a fourth disulfide bond with increased structural stability and retained function.

The intriguing structure of non‐geometric frames in string theory

Abstract: Non-geometric frames in string theory are related to the geometric ones by certain local O(D,D) transformations, the so-called $\beta$-transforms. For each such transformation, we show that there exists both a natural field redefinition of the metric and the Kalb-Ramond two-form as well as an associated Lie algebroid. We furthermore prove that the all-order low-energy effective action of the superstring, written in terms of the redefined fields, can be expressed through differential-geometric objects of the corresponding Lie algebroid. Thus, the latter provides a natural framework for effective superstring actions in non-geometric frames. Relations of this new formalism to double field theory and to the description of non-geometric backgrounds such as T-folds are discussed as well.