Retinal proteins as model systems for membrane protein folding

Experimental folding studies of membrane proteins are more challenging than water-soluble proteins because of the higher hydrophobicity content of membrane embedded sequences and the need to provide a hydrophobic milieu for the transmembrane regions. The first challenge is their denaturation: due to the thermodynamic instability of polar groups in the membrane, secondary structures in membrane proteins are more difficult to disrupt than in soluble proteins. The second challenge is to refold from the denatured states. Successful refolding of membrane proteins has almost always been from very subtly denatured states. Therefore, it can be useful to analyze membrane protein folding using computational methods, and we will provide results obtained with simulated unfolding of membrane protein structures using the Floppy Inclusions and Rigid Substructure Topography (FIRST) method. Computational methods have the advantage that they allow a direct comparison between diverse membrane proteins. We will review here both, experimental and FIRST studies of the retinal binding proteins bacteriorhodopsin and mammalian rhodopsin, and discuss the extension of the findings to deriving hypotheses on the mechanisms of folding of membrane proteins in general. This article is part of a Special Issue entitled: Retinal Proteins—You can teach an old dog new tricks.     

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

Most cellular processes are orchestrated by macromolecular complexes. However, structural elucidation of these endogenous complexes can be challenging because they frequently contain large numbers of proteins, are compositionally and morphologically heterogeneous, can be dynamic, and are often of low abundance in the cell. Here, we present a strategy for the structural characterization of such complexes that has at its center chemical cross-linking with mass spectrometric readout. In this strategy, we isolate the endogenous complexes using a highly optimized sample preparation protocol and generate a comprehensive, high-quality cross-linking dataset using two complementary cross-linking reagents. We then determine the structure of the complex using a refined integrative method that combines the cross-linking data with information generated from other sources, including electron microscopy, X-ray crystallography, and comparative protein structure modeling. We applied this integrative strategy to determine the structure of the native Nup84 complex, a stable hetero-heptameric assembly (∼600 kDa), 16 copies of which form the outer rings of the 50-MDa nuclear pore complex (NPC) in budding yeast. The unprecedented detail of the Nup84 complex structure reveals previously unseen features in its pentameric structural hub and provides information on the conformational flexibility of the assembly. These additional details further support and augment the protocoatomer hypothesis, which proposes an evolutionary relationship between vesicle coating complexes and the NPC, and indicates a conserved mechanism by which the NPC is anchored in the nuclear envelope.Macromolecular complexes are the building blocks that drive virtually all cellular and biological processes. In each eukaryotic cell, there exist many hundreds of these protein complexes (1–3), the majority of which are still poorly understood in terms of their structures, dynamics, and functions. The classical structure determination approaches of nuclear magnetic resonance, X-ray crystallography, and electron microscopy (EM)¹ remain challenged in attempts to determine the high-resolution structures of large, dynamic, and flexible complexes in a living cell (4). Thus, additional robust and rapid methods are needed, ideally working in concert with these classical approaches, to allow the greatest structural and functional detail in characterizations of macromolecular assemblies.Integrative modeling approaches help address this need, providing powerful tools for determining the structures of endogenous protein complexes (5, 6) by relying on the collection of an extensive experimental dataset, preferably coming from diverse sources (both classical and new) and different levels of resolution. These data are translated into spatial restraints that are used to calculate an ensemble of structures by satisfying the restraints, which in turn can be analyzed and assessed to determine precision and estimate accuracy (5, 7). A major advantage of this approach is that it readily integrates structural data from different methods and a wide range of resolutions, spanning from a few angstroms to dozens of nanometers. This strategy has been successfully applied to a number of protein complexes (8–16). However, it has proven difficult and time-consuming to generate a sufficient number of accurate spatial restraints to enable high-resolution structural characterization; thus, the determination of spatial restraints currently presents a major bottleneck for widespread application of this integrative approach. An important step forward is therefore the development of technologies for collecting high-resolution and information-rich spatial restraints in a rapid and efficient manner, ideally from endogenous complexes isolated directly from living cells.Chemical cross-linking with mass spectrometric readout (CX-MS) (17, 18) has recently emerged as an enabling approach for obtaining residue-specific restraints on the structures of proteins and protein complexes (19–25). In a CX-MS experiment, the purified protein complex is chemically conjugated by a functional group-specific cross-linker, and this is followed by proteolytic digestion and analysis of the resulting peptide mixture by mass spectrometry (MS). However, because of the complexity of the peptide mixtures and low abundance of most of the informative cross-linked species, comprehensive detection of these cross-linked peptides has proven challenging. This challenge increases substantially in studies of endogenous complexes of modest to low abundance, which encompass the great majority of assemblies in any cell (26, 27). In addition, because most cross-linkers used for CX-MS target primary amines, comprehensive detection of cross-links is further limited by the occurrence of lysine, which constitutes only ∼6% of protein sequences, although these lysine residues are generally present on protein surfaces. The use of cross-linkers with different chemistries and reactive groups, especially toward abundant residues, would increase the cross-linking coverage and could be of great help for downstream structural analysis (28).The nuclear pore complex (NPC) is one of the largest protein assemblies in the cell and is the sole mediator of macromolecular transport between the nucleus and the cytoplasm. The NPC is formed by multiple copies of ∼30 different proteins termed nucleoporins (Nups) that are assembled into discrete subcomplexes (8, 29). These building blocks are arranged into eight symmetrical units called spokes that are radially connected to form several concentric rings. The outer rings of the NPC are mainly formed by the Nup84 complex (a conserved complex, termed the Nup107–Nup160 complex in vertebrates). In budding yeast, the Nup84 complex is an essential, Y-shaped assembly of ∼600 kDa that is formed by seven nucleoporins (Nup133, Nup120, Nup145c, Nup85, Nup84, Seh1, and Sec13 in Saccharomyces cerevisiae) (30). The Nup84 complex has been shown to have a common evolutionary origin with vesicle coating complexes (VCCs), such as COPII, COPI, and clathrin (31, 32), but the evolutionary relationships between these VCCs have not been fully delineated. The Nup84 complex has been extensively characterized; several of its components have been analyzed via X-ray crystallography (33, 34), its overall shape has been defined by means of negative-stain electron microscopy (14, 30, 35, 36), and recently efforts were made to define the protein contacts in the Nup84 complex via CX-MS in humans (35) and a thermophilic fungus (37). Finally, we recently used an integrative modeling approach combining domain mapping, negative-stain electron microscopy (38), and publicly available crystal structures to generate a medium-resolution map of the native Nup84 complex (14). However, despite all these efforts, the fine features of the complex, and in particular the intricate domain orientations and contacts within the complex''s hub, remain poorly described.To address these issues, we present here an optimized CX-MS strategy for robust and in-depth structural characterization of endogenous protein complexes. To test the strategy, we generated a comprehensive high-quality CX-MS dataset on the endogenous Nup84 complex using two complementary cross-linkers, disuccinimidyl suberate (DSS) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC). Using the resulting cross-linking restraints together with other sources of information (including electron microscopy, X-ray crystallography, and comparative modeling), we computed a detailed structure of the endogenous Nup84 complex. In addition to providing the overall architecture of the yeast Nup84 complex, the resulting structure reveals the previously unknown architecture of its pentameric structural hub. Our results demonstrate that the present approach provides a robust framework for the standardized generation and use of CX-MS spatial restraints toward the structural characterization of endogenous protein complexes.     

Reliability of assessment of protein structure prediction methods

The reliability of ranking of protein structure modeling methods is assessed. The assessment is based on the parametric Student's t test and the nonparametric Wilcox signed rank test of statistical significance of the difference between paired samples. The approach is applied to the ranking of the comparative modeling methods tested at the fourth meeting on Critical Assessment of Techniques for Protein Structure Prediction (CASP). It is shown that the 14 CASP4 test sequences may not be sufficient to reliably distinguish between the top eight methods, given the model quality differences and their standard deviations. We suggest that CASP needs to be supplemented by an assessment of protein structure prediction methods that is automated, continuous in time, based on several criteria applied to a large number of models, and with quantitative statistical reliability assigned to each characterization.     

Nanocrystallization by Evaporative Antisolvent Technique for Solubility and Bioavailability Enhancement of Telmisartan

Telmisartan is an orally active nonpeptide angiotensin II receptor antagonist used in the management of hypertension. It is a Biopharmaceutics Classification System class II drug having aqueous solubility of 9.9 μg/ml. Telmisartan (TEL) nanocrystals were prepared by evaporative antisolvent precipitation technique using different stabilizers as PVPK30, TPGS, Poloxamer 188, and PEG 6000 in combination or singly. The nanosuspensions were characterized in terms of particle size distribution, zeta potential, and polydispersity index. The suspension containing PVPK30 and TPGS (1:1) showed least average particle size of 82.63 nm and polydispersity index of 0.472. The zeta potential of nanosuspensions ranged between 6.54 and 10.8 mV. An increase of 116.45% was evident in the specific surface area of the freeze-dried product. Contact angle of nanoparticles was also lowered to 27° as compared to 50.8° for TEL. Saturation solubility studies in various media revealed a significant increase in comparison to plain drug. An increase of 3.74× in saturation solubility in FaSSIF and 5.02× in FeSSIF was seen. In vitro dissolution profile of nanosuspension coated on pellets revealed release of 85% in water, 95% in 0.1 N HCl, and 75% in phosphate buffer in 30 min. Nanosuspensions were found to be stable in the presence of univalent and bivalent electrolytes. A tenfold increase in bioavailability was evident. Nanoparticles of telmisartan prepared by bottom-up technique proved to be effective in improving the oral bioavailability as a result of enhanced solubility and dissolution rate.Key words: biorelevant media, contact angle, specific surface area, telmisartan, TPGS     

Urine metabolomics reveals novel physiologic functions of human aldehyde oxidase and provides biomarkers for typing xanthinuria

Classical xanthinuria is a rare inherited metabolic disorder caused by either isolated xanthine dehydrogenase (XDH) deficiency (type I) or combined XDH and aldehyde oxidase (AO) deficiency (type II). XDH and AO are evolutionary related enzymes that share a sulfurated molybdopterin cofactor. While the role of XDH in purine metabolism is well established, the physiologic functions of AO are mostly unknown. XDH and AO are important drug metabolizing enzymes. Urine metabolomic analysis by high pressure liquid chromatography and mass spectrometry of xanthinuric patients was performed to unveil physiologic functions of XDH and AO and provide biomarkers for typing xanthinuria. Novel endogenous products of AO, hydantoin propionic acid, N1-methyl-8-oxoguanine and N-(3-acetamidopropyl) pyrrolidin-2-one formed in the histidine, nucleic acid and spermidine metabolic pathways, respectively, were identified as being lowered in type II xanthinuria. Also lowered were the known AO products, N1-methyl-2-pyridone-5-carboxamide and N1-methyl-4-pyridone-5-carboxamide in the nicotinamide degradation pathway. In contrast to the KEGG annotations, the results suggest minor role of human AO in the conversion of pyridoxal to pyridoxate and gentisaldehyde to gentisate in the vitamin B6 and tyrosine metabolic pathways, respectively. The perturbations in purine degradation due to XDH deficiency radiated further from the previously known metabolites, uric acid, xanthine and hypoxanthine to guanine, methyl guanine, xanthosine and inosine. Possible pathophysiological implications of the observed metabolic perturbations are discussed. The identified biomarkers have the potential to replace the allopurinol-loading test used in the past to type xanthinuria, thus facilitating appropriate pharmacogenetic counseling and gene directed search for causative mutations.     

Understanding protein folding via free-energy surfaces from theory and experiment

The ability of protein molecules to fold into their highly structured functional states is one of the most remarkable evolutionary achievements of biology. In recent years, our understanding of the way in which this complex self-assembly process takes place has increased dramatically. Much of the reason for this advance has been the development of energy surfaces (landscapes), which allow the folding reaction to be described and visualized in a meaningful manner. Analysis of these surfaces, derived from the constructive interplay between theory and experiment, has led to the development of a unified mechanism for folding and a recognition of the underlying factors that control the rates and products of the folding process.     

Evidence for a Shared Nuclear Pore Complex Architecture That Is Conserved from the Last Common Eukaryotic Ancestor

The nuclear pore complex (NPC) is a macromolecular assembly embedded within the nuclear envelope that mediates bidirectional exchange of material between the nucleus and cytoplasm. Our recent work on the yeast NPC has revealed a simple modularity in its architecture and suggested a common evolutionary origin of the NPC and vesicle coating complexes in a progenitor protocoatomer. However, detailed compositional and structural information is currently only available for vertebrate and yeast NPCs, which are evolutionarily closely related. Hence our understanding of NPC composition in a full evolutionary context is sparse. Moreover despite the ubiquitous nature of the NPC, sequence searches in distant taxa have identified surprisingly few NPC components, suggesting that much of the NPC may not be conserved. Thus, to gain a broad perspective on the origins and evolution of the NPC, we performed proteomics analyses of NPC-containing fractions from a divergent eukaryote (Trypanosoma brucei) and obtained a comprehensive inventory of its nucleoporins. Strikingly trypanosome nucleoporins clearly share with metazoa and yeast their fold type, domain organization, composition, and modularity. Overall these data provide conclusive evidence that the majority of NPC architecture is indeed conserved throughout the Eukaryota and was already established in the last common eukaryotic ancestor. These findings strongly support the hypothesis that NPCs share a common ancestry with vesicle coating complexes and that both were established very early in eukaryotic evolution.Nearly all eukaryotic cells possess an extensive endomembrane system that is principally responsible for protein targeting and modification (1). The nucleus, the defining eukaryotic feature, is separated from the cytoplasm by a double bilayered nuclear envelope (NE)¹ that is contiguous with the rest of this endomembrane system via connections to the endoplasmic reticulum. Nuclear pore complexes (NPCs) fenestrate the NE, serving as the exclusive sites mediating exchange between the nucleoplasmic and cytoplasmic compartments. Macromolecules are chaperoned through the NPC by numerous transport factors. It has been proposed that the endomembrane system and nucleus have an autogenous origin (i.e. evolving from invaginations of an ancestral plasma membrane) and were established early in eukaryotic evolution (2).The composition of the NPC has been cataloged at ∼30 distinct nucleoporins (Nups) (3) for the yeast Saccharomyces cerevisiae (4) and vertebrates (5), two members of the Opisthokonta (animals, fungi, and closely related protists). Ultrastructural studies have identified objects morphologically similar (at a first approximation) to opisthokont NPCs in the other major eukaryote supergroups (6–8). However, very few data are available concerning the detailed NPC molecular composition and architecture for nearly all eukaryotic lineages, leaving a relatively narrow view of the “typical” NPC and its origins. A few examples of potential Nup orthologs beyond the opisthokonts have been reported, leading to the suggestion that substantial portions of the NPC may have an ancient, pre-last common eukaryotic ancestor (LCEA) origin (9). However, a more extensive study has concluded that LCEA possessed a primitive ancestral NPC that passed few components to its modern descendants (10).In yeast and vertebrates, the NPC consists of an eight-spoked core surrounding a central tube that serves as the conduit for macromolecular exchange. Each spoke can be divided into two similar nucleoplasmic and cytoplasmic halves. The eight spokes connect to form several coaxial rings: the membrane rings, the two outer rings at the nucleoplasmic and cytoplasmic periphery, and the two adjacent inner rings (11). Groups of Nups that we term “linker Nups” are attached between both sets of outer and inner rings. Another group of related proteins, collectively termed phenylalanine-glycine (FG) Nups, are largely exposed on the inner surface of the spokes and anchored either to the inner rings or to the linker Nups (11).Opisthokont Nups can be grouped into three structural classes (11, 12). The first class comprises membrane-bound proteins that anchor the NPC into the NE. The second class is the core scaffold Nups; these proteins constitute the bulk of the NPC mass, form the central tube, and provide the scaffold for the deployment of the third class of Nups across both faces of the NPC. The core scaffold Nups are remarkably restricted at the structural level and contain only three distinct arrangements of 2-fold types: proteins dominated by an α-solenoid fold (also termed a helix-turn-helix repeat domain), proteins consisting of a β-propeller fold, and finally proteins composed of an amino-terminal β-propeller fold followed by a carboxyl-terminal α-solenoid fold (which we here term a β-α structure) (12). FG Nups comprise the third class. These Nups carry multiply repeated degenerate “Phe-Gly” motifs (FG repeats) separated by hydrophilic or charged residues that form large unstructured domains. Each FG Nup also contains a small structured domain (often a coiled coil motif) that serves as the anchor site for interaction with the remainder of the NPC.Many transport factors belong to a structurally related protein family collectively termed karyopherins (Kaps) (13, 14). Transport across the NPC depends on the interactions between Kaps, cargo molecules, and the disordered repeat domains of FG Nups; the latter are thought to form the selective barrier for nucleocytoplasmic transport, guiding the Kap·cargo complexes (and other transport factors) through the central tube while excluding other macromolecules (for reviews, see Refs. 3 and 15–22).Significantly we have previously noted that the fold composition and arrangement of many of the core scaffold Nups are shared with proteins that form coating structures that participate in the generation and transport of vesicles between different endomembrane compartments; significantly many vesicle coating complex proteins and NPC scaffold Nups share an α-solenoid fold, β-propeller fold, or β-α structure (12, 23–28). These similarities gave rise to the “protocoatomer hypothesis,” which suggests a common ancestry for the NPC and these vesicle coat complexes. However, it is unclear how many, if any, of these particular core scaffold Nups are widely conserved, and hence it is unclear how general this potential relationship is throughout the Eukaryota. Thus, two scenarios are possible. The first is that the coatomer-like proteins are only found in a subset of the eukaryotes (including the opisthokonts), indicating that they are a relatively recent acquisition of only some eukaryotes and are not a general feature of all NPCs. The second is that the coatomer-like proteins are conserved in all eukaryotes, providing strong support to the protocoatomer hypothesis. To directly address this issue we characterized the NPC of Trypanosoma brucei, a highly divergent but experimentally tractable organism, using proteomics. The resulting data indicate an ancient origin for the majority of the NPC components and shed light on the origin of LCEA itself.     

How well can the accuracy of comparative protein structure models be predicted?

Comparative structure models are available for two orders of magnitude more protein sequences than are experimentally determined structures. These models, however, suffer from two limitations that experimentally determined structures do not: They frequently contain significant errors, and their accuracy cannot be readily assessed. We have addressed the latter limitation by developing a protocol optimized specifically for predicting the Calpha root-mean-squared deviation (RMSD) and native overlap (NO3.5A) errors of a model in the absence of its native structure. In contrast to most traditional assessment scores that merely predict one model is more accurate than others, this approach quantifies the error in an absolute sense, thus helping to determine whether or not the model is suitable for intended applications. The assessment relies on a model-specific scoring function constructed by a support vector machine. This regression optimizes the weights of up to nine features, including various sequence similarity measures and statistical potentials, extracted from a tailored training set of models unique to the model being assessed: If possible, we use similarly sized models with the same fold; otherwise, we use similarly sized models with the same secondary structure composition. This protocol predicts the RMSD and NO3.5A errors for a diverse set of 580,317 comparative models of 6174 sequences with correlation coefficients (r) of 0.84 and 0.86, respectively, to the actual errors. This scoring function achieves the best correlation compared to 13 other tested assessment criteria that achieved correlations ranging from 0.35 to 0.71.     

"Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms

Background  

A wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. These include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. It has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. In this work, protein crystal structures from hyper/thermophilic organisms and their mesophilic homologs have been compared, in order to quantify the difference of apolar contact area and to assess the role played by the hydrophobic contacts in the stabilization of the protein core, at high temperatures.