AMP-activated protein kinase: structure and regulation

Mammalian AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that acts as a sensor of cellular energy status. It is activated by a large variety of cellular stresses that increase cellular AMP and decrease ATP levels and also by physiological stimuli, such as muscle contraction, or by hormones such as leptin and adiponectin. AMPK modulates multiple metabolic pathways. As a result, it has become a target for the development of new drugs for the treatment of type II diabetes, obesity or even cancer. In fact, it has been recently reported that drugs used in the treatment of diabetes, such as metformin and thiazolidinediones (TZDs), exert their beneficial effects through the activation of AMPK. AMPK is a heterotrimeric complex composed of a catalytic subunit (AMPK-alpha) and two regulatory subunits (AMPK-beta and AMPK-gamma). Functional orthologues of this kinase complex are found throughout eukaryotic kingdom, from yeast to humans, indicating that the function of this complex is evolutionarily conserved. This review summarizes the recent studies on the structure and regulation of the AMPK heterotrimeric complex.     

Peptide Self-Assembly into Amyloid Fibrils at Hard and Soft Interfaces—From Corona Formation to Membrane Activity

Peptides and proteins are exposed to a variety of interfaces in a physiological environment, such as cell membranes, protein nanoparticles (NPs), or viruses. These interfaces have a significant impact on the interaction, self-assembly, and aggregation mechanisms of biomolecular systems. Peptide self-assembly, particularly amyloid fibril formation, is associated with a wide range of functions; however, there is a link with neurodegenerative diseases, such as Alzheimer's disease. This review highlights how interfaces affect peptide structure and the kinetics of aggregation leading to fibril formation. In nature, many surfaces are nanostructures, such as liposomes, viruses, or synthetic NPs. Once exposed to a biological medium, nanostructures are coated with a corona, which then determines their activity. Both accelerating and inhibiting effects on peptide self-assembly have been observed. When amyloid peptides adsorb to a surface, they typically concentrate locally, which promotes aggregation into insoluble fibrils. Starting from a combined experimental and theoretical approach, models that allow for a better understanding of peptide self-assembly near hard and soft matter interfaces are introduced and reviewed. Research results from recent years are presented and relationships between biological interfaces, such as membranes and viruses, and amyloid fibril formation are proposed.     

A first step towards the understanding of the 5-HT(3) receptor subunit heterogeneity from a computational point of view

The functional serotonin type-3 receptor (5-HT(3)-R), which is the target of many neuroactive drugs, is known to be a homopentamer made of five identical subunits A (5-HT(3A)-R) or a binary heteropentamer made of subunits A and B (5-HT(3A/B)-R) with a still debated arrangement and stoichiometry. This complex picture has been recently further complicated by the discovery of additional 5-HT(3)-R subunits, C, D, and E, which, similarly to the B subunit, are apparently able to form functional receptors only if co-expressed with subunit A. Being the binding site for both serotonin and antagonists (i.e. drugs) located at the extracellular interface between two adjacent subunits, the large variability of the 5-HT(3)-R composition becomes a crucial issue, since it can originate many different interfaces providing non-equivalent ligand binding sites and complicating the pharmacological modulation. Here, the different 5-HT(3)-R interfaces are analysed, on the bases of the structural conformations of previously built 3D homology models and of the known subunit sequences, by addressing their physicochemical characterization. The results confirm the presence of an aromatic cluster located in the core of the A-A interface as a key determinant for having an interface both stable and functional. This is used as a discriminant to make hypotheses about the capability of all the other possible interfaces constituted by the known 5-HT(3)-R sequences A, B, C, D, and E to build active receptors.     

Structures of BaF2-CaF2 heterolayers and their influences on ionic conductivity

Recently, artificial ion conductors have been prepared by growing epitaxial heterolayers consisting of BaF2-CaF2 using molecular beam epitaxy. The ionic conductivity of these heterolayers shows a strong dependence on the layer thickness [N. Sata, S. Eberman, K. Eberl, and J. Maier, Nature 408, 996 (2000)]. In this paper three such heterolayers with different spacings (sample A: 80 nm, sample B: 10 nm, sample C: 1 nm) are investigated by conventional transmission electron microscopy and high-resolution transmission electron microscopy. The spacings are chosen such that they fall into the three conductivity regimes observed in N. Sata et al. (l > 50 nm; 8 < l < 50 nm; l < 8 nm). In accordance with conductivity studies, the samples with spacings of 10 nm or greater (A,B) are epitaxial and continuous, whereas in the case of extremely small spacing (C) the continuity of the layers is destroyed by formation of a column-like structure. Analytical electron microscopy reveals that, instead of forming multilayers, Ca and Ba separate in different columns in sample C. The structure properties of sample A (large l) are quite ideal: Planar interfaces with regular arrays of misfit dislocations with their Burgers vectors on the interface are observed. In the case of sample B (medium l) the lattice misfit is accommodated, in addition, by wavy interfaces associated with dislocations characterized by a Burgers vector that makes a large angle to the interfaces. The (111) lattice spacing very close to the interfaces is markedly changed due to this novel relaxation mechanism in the multilayer. The influences of the crystallographic defects on the ionic conductivity are also discussed.     

Lattice modeling: Accuracy of energy calculations

Energy calculations based on lattice models of protein chains are always approximate, because any such a model distorts distances between chain links and, consequently, the energies of interaction between them. The energetic errors of lattice models are examined here for 15 proteins of different sizes and types of secondary structure, for lattice spacings ranging from 0.25 to 2.5 Å. The lattice models are derived using previously described algorithms which insure a minimal root mean square (rms) deviation from the off-lattice structure for any given lattice-protein orientation. For each protein structure we computed a set of different lattice models with virtually equal rms deviations, and then compared their energies. Energy calculations were based on the pairwise potentials. We found that the energies of lattice models follows a normal distribution with a nonnegligible dispersion, even at a fine lattice spacing of 0.25 Å. For any lattice model of a protein, the lattice spacing must be 1.0 Å or less in order to be able to distinguish energetically between the folded and extended states. However, when an ensemble of lattice models is considered, this distinction can be made for lattice spacing up to 2.0 Å. We conclude that to attain a better approximation of the protein lattice model energies, one must adjust potentials to the lattice spacing. © 1996 by John Wiley & Sons, Inc.     

Interfacial shear rheology of protein-surfactant layers

The shear rheology of adsorbed or spread layers at air/liquid and liquid/liquid phase boundaries is relevant in a wide range of technical applications such as mass transfer, monolayers, foaming, emulsification, oil recovery, or high speed coating. Interfacial shear rheological properties can provide important information about interactions and molecular structure in the interfacial layer. A variety of measuring techniques have been proposed in the literature to measure interfacial shear rheological properties and have been applied to pure protein or mixed protein adsorption layers at air/water or oil/water interfaces. Such systems play for example an important role as stabilizers in foams and emulsions. The aim of this contribution is to give a literature overview of interfacial shear rheological studies of pure protein and protein/surfactant mixtures at liquid interfaces measured with different techniques. Techniques which utilize the damping of waves, spectroscopic or AFM techniques and all micro-rheological techniques will not discuss here.     

Characteristics of amyloid-related oligomers revealed by crystal structures of macrocyclic β-sheet mimics

Protein amyloid oligomers have been strongly linked to amyloid diseases and can be intermediates to amyloid fibers. β-Sheets have been identified in amyloid oligomers. However, because of their transient and highly polymorphic properties, the details of their self-association remain elusive. Here we explore oligomer structure using a model system: macrocyclic peptides. Key amyloidogenic sequences from Aβ and tau were incorporated into macrocycles, thereby restraining them to β-strands, but limiting the growth of the oligomers so they may crystallize and cannot fibrillate. We determined the atomic structures for four such oligomers, and all four reveal tetrameric interfaces in which β-sheet dimers pair together by highly complementary, dry interfaces, analogous to steric zippers found in fibers, suggesting a common structure for amyloid oligomers and fibers. In amyloid fibers, the axes of the paired sheets are either parallel or antiparallel, whereas the oligomeric interfaces display a variety of sheet-to-sheet pairing angles, offering a structural explanation for the heterogeneity of amyloid oligomers.     

X-ray studies and time-resolved photoluminescence on optically pumped antimonide-based midinfrared type-II lasers

We report on high-resolution X-ray diffraction and time-resolved photoluminescence (TR-PL) studies of antimonide-based midinfrared (MIR) type-II laser samples. A structural characterization taking into account asymmetrical strain, layer tilting, and relaxation enables an accurate determination of the average lattice constant of the active region and the composition of the cladding layers. By designing the antimonide-to-arsenide interfaces, we achieve exact lattice matching of the active region to the substrate. Non-radiative recombination processes are investigated with time-resolved photoluminescence. The samples are also characterized under optically pumped laser operation. By an examination of the time-integrated and time-resolved amplified spontaneous emission (TR-ASE), we investigate the modal gain and gain dynamics. The variable stripe length method is combined with the TR-PL approach. Compared to the time-integrated gain spectra the spectral dependence of the maximum and minimum time-resolved gain shows a broad plateau. The full width half maximum (FWHM) of the TR-ASE pulse is 5.5 +/- 0.5 ps. Thus, short pulses in this range should be achievable upon laser operation. The active regions of the laser structures investigated here are promising subunits of type-II quantum cascade lasers.     

A large decoy set of protein–protein complexes produced by flexible docking

Computational methods are needed to help characterize the structure and function of protein–protein complexes. To develop and improve such methods, standard test problems are essential. One important test is to identify experimental structures from among large sets of decoys. Here, a flexible docking procedure was used to produce such a large ensemble of decoy complexes. In addition to their use for structure prediction, they can serve as a proxy for the nonspecific, protein–protein complexes that occur transiently in the cell, which are hard to characterize experimentally, yet biochemically important. For 202 homodimers and 41 heterodimers with known X‐ray structures, we produced an average of 1217 decoys each. The structures were characterized in detail. The decoys have rather large protein–protein interfaces, with at least 45 residue–residue contacts for every 100 contacts found in the experimental complex. They have limited intramonomer deformation and limited intermonomer steric conflicts. The decoys thoroughly sample each monomer's surface, with all the surface amino acids being part of at least one decoy interface. The decoys with the lowest intramonomer deformation were analyzed separately, as proxies for nonspecific protein–protein complexes. Their interfaces are less hydrophobic than the experimental ones, with an amino acid composition similar to the overall surface composition. They have a poorer shape complementarity and a weaker association energy, but are no more fragmented than the experimental interfaces, with 2.1 distinct patches of interacting residues on average, compared to 2.6 for the experimental interfaces. The decoys should be useful for testing and parameterizing docking methods and scoring functions; they are freely available as PDB files at http://biology.polytechnique.fr/decoys . © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

The instabilities of the Hartree–Fock solutions and the lattice instabilities for conjugated hydrocarbons: The bond-order and bond-length alternations

The instabilities, especially the singlet instabilities, of the conventional Hartree–Fock (HF ) solutions for a variety of alternant and nonalternant hydrocarbons, some of which have been known to show lattice instabilities (bond-length alterations), are examined. The HF solutions for nonalternant hydrocarbons in the pentalene series larger than heptalene and [4n + 2]-annulenes larger than C₂₂H₂₂ are found to be singlet unstable and there appear new solutions lower in energy than the conventional HF solutions and characterized by charge-density waves exhibiting bond-order alterations. It is found that such symmetry-breaking solutions are energetically further stabilized by distorting the nuclear framework so that it may match up with the distribution of bond-order matrix elements of the charge-density wave, which means that in conjugated systems the singlet instability of the HF solution is always accompanied with the lattice instability. Further, it is shown that in conjugated systems, even when the HF solution is singlet stable, if it is not sufficiently stable as, for example, in pentalene and heptalene, there is every possibility for the occurrence of lattice instability. It is also shown that the singlet instability as well as the lattice instability arises from the existence of a sufficiently low-lying singlet excited state.     

Controlling molecular crystal polymorphism with self-assembled monolayer templates

The control of crystal polymorphism is a long-standing issue in solid-state chemistry, which has many practical implications for a variety of commercial applications. At least four different crystalline forms of 1,3-bis(m-nitrophenyl) urea (MNPU), a classic molecular crystal system, are known to crystallize from solution in various concomitant combinations. Herein we demonstrate that the introduction of gold-thiol self-assembled monolayers (SAMs) of substituted 4'-X-mercaptobiphenyls (X = H, I, and Br) into the crystallization solution can serve as an effective means to selectively template the nucleation and growth of alpha-, beta-, and gamma-MNPU phases, respectively. Polymorph control in the presence of SAM surfaces persists under a variety of solution conditions and consistently results in crystalline materials with high phase purity. The observed selectivity is rationalized on the basis of long-range two-dimensional geometric lattice matching and local complementary chemical interactions at the SAM/crystal interfaces.     

Recombinant drugs-on-a-chip: The usage of capillary electrophoresis and trends in miniaturized systems – A review

We present here a critical review covering conventional analytical tools of recombinant drug analysis and discuss their evolution towards miniaturized systems foreseeing a possible unique recombinant drug-on-a-chip device. Recombinant protein drugs and/or pro-drug analysis require sensitive and reproducible analytical techniques for quality control to ensure safety and efficacy of drugs according to regulatory agencies. The versatility of miniaturized systems combined with their low-cost could become a major trend in recombinant drugs and bioprocess analysis. Miniaturized systems are capable of performing conventional analytical and proteomic tasks, allowing for interfaces with other powerful techniques, such as mass spectrometry. Microdevices can be applied during the different stages of recombinant drug processing, such as gene isolation, DNA amplification, cell culture, protein expression, protein separation, and analysis. In addition, organs-on-chips have appeared as a viable alternative to testing biodrug pharmacokinetics and pharmacodynamics, demonstrating the capabilities of the miniaturized systems. The integration of individual established microfluidic operations and analytical tools in a single device is a challenge to be overcome to achieve a unique recombinant drug-on-a-chip device.     

Protein folding at emulsion oil/water interfaces

It has long been known that proteins change their conformation upon adsorption to emulsion oil/water interfaces. However, it is only recently that details of the specifics of these structural changes have emerged. The development of synchrotron radiation circular dichroism (SRCD), combined with advances in FTIR spectroscopy, has allowed the secondary and tertiary structure of proteins adsorbed at emulsion oil/water interfaces to be studied. SRCD in particular has provided quantitative information and has enabled new insights into the mechanisms and forces driving protein structure re-arrangement to be achieved.The extent of conformational re-arrangement of proteins at emulsion interfaces is influenced by several factors including; the inherit flexibility of the protein, the distribution of hydrophobic/hydrophilic domains within the protein sequence and the hydrophobicity of the oil phase. In general, proteins lose much of their tertiary structure upon adsorption to the oil/water interface and have considerable amounts of non-native secondary structure. Two key conformations have been identified in the structure of proteins at interfaces, intermolecular β-sheet and α-helix. The preferred conformation appears to be the α-helix which is the most compact amphipathic conformation at the oil/water interface. The polarity of the oil phase can have a considerable influence on the degree of protein conformational re-arrangement because it acts as a solvent for hydrophobic amino acids. The new conformation of proteins at interfaces also means that proteins undergo less heat induced re-arrangement at interfaces than in solution. Different conformations of proteins at interfaces impact on emulsification capability, emulsion stability and protein/emulsion digestion. Hence advances in the understanding of protein conformation at interfaces can help to identify suitable proteins and conditions for the preparation of emulsion based food products.     

Protein adsorption at the electrified air-water interface: implications on foam stability

The surface chemistry of ions, water molecules, and proteins as well as their ability to form stable networks in foams can influence and control macroscopic properties such as taste and texture of dairy products considerably. Despite the significant relevance of protein adsorption at liquid interfaces, a molecular level understanding on the arrangement of proteins at interfaces and their interactions has been elusive. Therefore, we have addressed the adsorption of the model protein bovine serum albumin (BSA) at the air-water interface with vibrational sum-frequency generation (SFG) and ellipsometry. SFG provides specific information on the composition and average orientation of molecules at interfaces, while complementary information on the thickness of the adsorbed layer can be obtained with ellipsometry. Adsorption of charged BSA proteins at the water surface leads to an electrified interface, pH dependent charging, and electric field-induced polar ordering of interfacial H(2)O and BSA. Varying the bulk pH of protein solutions changes the intensities of the protein related vibrational bands substantially, while dramatic changes in vibrational bands of interfacial H(2)O are simultaneously observed. These observations have allowed us to determine the isoelectric point of BSA directly at the electrolyte-air interface for the first time. BSA covered air-water interfaces with a pH near the isoelectric point form an amorphous network of possibly agglomerated BSA proteins. Finally, we provide a direct correlation of the molecular structure of BSA interfaces with foam stability and new information on the link between microscopic properties of BSA at water surfaces and macroscopic properties such as the stability of protein foams.     

Novel insights into V-ATPase functioning: distinct roles for its accessory subunits ATP6AP1/Ac45 and ATP6AP2/(pro) renin receptor

The vacuolar (H+)-ATPase (V-ATPase) is a universal proton pump and its activity is required for a variety of cell-biological processes such as membrane trafficking, receptor-mediated endocytosis, lysosomal protein degradation, osteoclastic bone resorption and maintenance of acid-base homeostasis by renal intercalated cells. In neuronal and neuroendocrine cells, the V-ATPase is the major regulator of intragranular acidification which is indispensable for correct prohormone processing and neurotransmitter uptake. In these specialized cells, the V-ATPase is equipped with the accessory subunits ATP6AP1/Ac45 and ATP6AP2/(pro) renin receptor. Recent studies have shown that Ac45 interacts with the V0- sector of the V-ATPase complex, thereby regulating the intragranular pH and Ca2+-dependent exocytotic membrane fusion. Thus, Ac45 can be considered as a V-ATPase regulator in the neuroendocrine secretory pathway. ATP6AP2 has recently been found to be identical to the (pro) renin receptor and has a dual role: (i) in the renin-angiotensin system that also regulates V-ATPase activity; (ii) acting as an adapter by binding to both the V-ATPase and the Wnt receptor complex, thereby recruiting the receptor complex into an acidic microenvironment. We here provide an overview of the two V-ATPase accessory subunits as novel key players in V-ATPase regulation. We argue that the accessory subunits are candidate genes for V-ATPase-related human disorders and promising targets for manipulating V-ATPase functioning in vivo.     

Search strategies in structural bioinformatics

Optimisation problems pervade structural bioinformatics. In this review, we describe recent work addressing a selection of bioinformatics challenges. We begin with a discussion of research into protein structure comparison, and highlight the utility of Kolmogorov complexity as a measure of structural similarity. We then turn to research into de novo protein structure prediction, in which structures are generated from first principles. In this endeavour, there is a compromise between the detail of the model and the extent to which the conformational space of the protein can be sampled. We discuss some developments in this area, including off-lattice structure prediction using the great deluge algorithm. One strategy to reduce the size of the search space is to restrict the protein chain to sites on a regular lattice. In this context, we highlight the use of memetic algorithms, which combine genetic algorithms with local optimisation, to the study of simple protein models on the two-dimensional square lattice and the face-centred cubic lattice.     

Capillary electrophoresis for analysis of microheterogeneous glutelin subunits in rice (Oryza sativa L.)

Glutelin, the major storage protein of rice seed, consists of microheterogenous subunits and partially exists in a macromolecular form that is polymerized by intersubunit disulfide bonds. In order to analyze the glutelin subunits using high-throughput CE, we first identified a sample preparation procedure suitable for CE. The polymerized glutelin treated with a reductant could not dissociate into its constituent monomer subunits when it was dissolved in an acidic solution. However, the glutelin dissociated into its subunits and component α and β polypeptides when it was denatured and reduced by an appropriate amount of urea and 2-mercaptoethanol at a specific incubation time and temperature. The molecular species of the completely dissociated α and β polypeptides were identified and quantitatively analyzed by CE using glutelin mutants. The CE analysis also demonstrated that the actual subunit variation in terms of the charge and/or size of the β polypeptides is much smaller than predicted when compared with that of α polypeptides, even under denaturing and reducing condition. Thus, the combined analytical system described here will be useful for basic and applied research, such as the kinetic characterization of higher-order structure and the quantitative evaluation of glutelin in a large number of diverse rice varieties.     

Triggers for β-sheet formation at the hydrophobic-hydrophilic interface: high concentration, in-plane orientational order, and metal ion complexation

Amyloid formation plays a causative role in neurodegenerative diseases such as Alzheimer's disease or Parkinson's disease. Soluble peptides form β-sheets that subsequently rearrange into fibrils and deposit as amyloid plaques. Many parameters trigger and influence the onset of the β-sheet formation. Early stages are recently discussed to be cell-toxic. Aiming at understanding various triggers such as interactions with hydrophobic-hydrophilic interfaces and metal ion complexation and their interplay, we investigated a set of model peptides at the air-water interface. We are using a general approach to a variety of diseases such as Alzheimer's disease, Parkinson's disease, and type II diabetes that are connected to amyloid formation. Surface sensitive techniques combined with film balance measurements have been used to assess the conformation of the peptides and their orientation at the air-water interface (IR reflection-absorption spectroscopy). Additionally, the structures of the peptide layers were characterized by grazing incidence X-ray diffraction and X-ray reflectivity. The peptides adsorb to the air-water interface and immediately adopt an α-helical conformation. This helical intermediate transforms into β-sheets upon further triggering. The factors that result in β-sheet formation are dependent on the peptide sequence. In general, the interface has the strongest effect on peptide conformation compared to high concentrations or metal ions. Metal ions are able to prevent aggregation in bulk but not at the interface. At the interface, metal ion complexation has only minor effects on the peptide secondary structure, influencing the in-plane structure that is formed in two dimensions. At the air-water interface, increased concentrations or a parallel arrangement of the α-helical intermediates are the most effective triggers. This study reveals the role of various triggers for β-sheet formation and their complex interplay. Our main finding is that the hydrophobic-hydrophilic interface largely governs the conformation of peptides. Therefore, the present study implies that special care is needed when interpreting data that may be affected by different amounts or types of interfaces during experimentation.