Computational design of a protein crystal

Protein crystals have catalytic and materials applications and are central to efforts in structural biology and therapeutic development. Designing predetermined crystal structures can be subtle given the complexity of proteins and the noncovalent interactions that govern crystallization. De novo protein design provides an approach to engineer highly complex nanoscale molecular structures, and often the positions of atoms can be programmed with sub-Å precision. Herein, a computational approach is presented for the design of proteins that self-assemble in three dimensions to yield macroscopic crystals. A three-helix coiled-coil protein is designed de novo to form a polar, layered, three-dimensional crystal having the P6 space group, which has a “honeycomb-like” structure and hexameric channels that span the crystal. The approach involves: (i) creating an ensemble of crystalline structures consistent with the targeted symmetry; (ii) characterizing this ensemble to identify “designable” structures from minima in the sequence-structure energy landscape and designing sequences for these structures; (iii) experimentally characterizing candidate proteins. A 2.1 Å resolution X-ray crystal structure of one such designed protein exhibits sub-Å agreement [backbone root mean square deviation (rmsd)] with the computational model of the crystal. This approach to crystal design has potential applications to the de novo design of nanostructured materials and to the modification of natural proteins to facilitate X-ray crystallographic analysis.     

Clinical anatomy of vertebrae in scoliosis: global analysis in four different diseases by multiplanar reconstructive computed tomography

Background contextFew accurate analyses of clinically useful vertebral anatomy have been conducted, and most have focused on thoracic idiopathic scoliosis.PurposeTo evaluate the different anatomic characteristics in scoliosis by disease type and level.Study designObservational cohort study.Patient sampleForty-eight patients with scoliosis were included in this study.Outcome measuresSubjects underwent computed tomography (CT) of the whole spine.MethodsForty-eight patients with scoliosis were included in this study: 15 adolescent idiopathic, 11 cerebral palsy (CP), 10 muscular dystrophy (MD), and 12 congenital (CG) scoliosis patients with similar demographics. Subjects underwent CT of the whole spine, preoperatively. Eight anatomic parameters were measured in multiplanar reconstructive CT images, and statistical analysis was performed to investigate differences.ResultsIn general, values in the anatomic parameters were similar for the four diseases. Each parameter showed the unique change pattern according to the spinal level regardless of curvature shape, direction, or magnitude. In particular, chord length (CL) in MD and CG scoliosis was lower than in adolescent idiopathic scoliosis (AIS) and CP, and pedicle rib unit length was lower in CG scoliosis than in the other diseases (p<.05). Comparisons of convex and concave anatomies in AIS showed that inner pedicle width (PWI) and outer pedicle width (PWO) were wider for convex side, CL, pedicle width, and transverse pedicle angle were greater for concave side (p<.05), and differences were more significant at apices. However, in CP, PWI and PWO were similar between convex and concaves sides (p>.05). Although PWI and PWO were wider for convex sides and CL and pedicle length were greater for concave sides in MD (p<.05), differences were less significant at apices. Particularly, CG scoliosis showed severely deformed anatomy, with differences of seven parameters at apical vertebrae (p<.05).ConclusionClinical anatomies of vertebrae in scoliosis were found to differ significantly at different levels and in terms of convexity and disease type.     

Ultrafast folding of alpha3D: a de novo designed three-helix bundle protein

Here, we describe the folding/unfolding kinetics of alpha3D, a small designed three-helix bundle. Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single-exponential process consistent with a minimal folding time of 3.2 +/- 1.2 micros (at approximately 50 degrees C), indicating that a protein can fold on the 1- to 5-micros time scale. Furthermore, the single-exponential nature of the relaxation indicates that the prefactor for transition state (TS)-folding models is probably >or=1 (micros)-1 for a protein of this size and topology. Molecular dynamics simulations and IR spectroscopy provide a molecular rationale for the rapid, single-exponential folding of this protein. alpha3D shows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways.     

Design of three-dimensional domain-swapped dimers and fibrous oligomers

Three-dimensional (3D) domain-swapped proteins are intermolecularly folded analogs of monomeric proteins; both are stabilized by the identical interactions, but the individual domains interact intramolecularly in monomeric proteins, whereas they form intermolecular interactions in 3D domain-swapped structures. The structures and conditions of formation of several domain-swapped dimers and trimers are known, but the formation of higher order 3D domain-swapped oligomers has been less thoroughly studied. Here we contrast the structural consequences of domain swapping from two designed three-helix bundles: one with an up-down-up topology, and the other with an up-down-down topology. The up-down-up topology gives rise to a domain-swapped dimer whose structure has been determined to 1.5 A resolution by x-ray crystallography. In contrast, the domain-swapped protein with an up-down-down topology forms fibrils as shown by electron microscopy and dynamic light scattering. This demonstrates that design principles can predict the oligomeric state of 3D domain-swapped molecules, which should aid in the design of domain-swapped proteins and biomaterials.     

De novo design of catalytic proteins

The de novo design of catalytic proteins provides a stringent test of our understanding of enzyme function, while simultaneously laying the groundwork for the design of novel catalysts. Here we describe the design of an O(2)-dependent phenol oxidase whose structure, sequence, and activity are designed from first principles. The protein catalyzes the two-electron oxidation of 4-aminophenol (k(cat)/K(M) = 1,500 M(-1).min(-1)) to the corresponding quinone monoimine by using a diiron cofactor. The catalytic efficiency is sensitive to changes of the size of a methyl group in the protein, illustrating the specificity of the design.     

Successful Aortic Valve Replacement Surgery in a Patient with Severe Haemophilia a with Low Titre Inhibitor

Acute leukemia, secondary myelodysplasia and paroxysmal nocturnal hemoglobinuria evolving from severe aplastic anemia (AA) following immunosuppressive therapy are well recognized. However, severe AA occurring after complete remission of acute promyelocytic leukemia (APL) has been documented only once in 2009. We report a case of 30-year-old male diagnosed with APL who achieved complete cytogenetic remission with all-trans retinoic acid based induction regimen and developed severe AA few months later during maintenance therapy.     

Soluble TREM2 inhibits secondary nucleation of Aβ fibrillization and enhances cellular uptake of fibrillar Aβ

Triggering receptor expressed on myeloid cells 2 (TREM2) is a single-pass transmembrane receptor of the immunoglobulin superfamily that is secreted in a soluble (sTREM2) form. Mutations in TREM2 have been linked to increased risk of Alzheimer’s disease (AD). A prominent neuropathological component of AD is deposition of the amyloid-β (Aβ) into plaques, particularly Aβ40 and Aβ42. While the membrane-bound form of TREM2 is known to facilitate uptake of Aβ fibrils and the polarization of microglial processes toward amyloid plaques, the role of its soluble ectodomain, particularly in interactions with monomeric or fibrillar Aβ, has been less clear. Our results demonstrate that sTREM2 does not bind to monomeric Aβ40 and Aβ42, even at a high micromolar concentration, while it does bind to fibrillar Aβ42 and Aβ40 with equal affinities (2.6 ± 0.3 µM and 2.3 ± 0.4 µM). Kinetic analysis shows that sTREM2 inhibits the secondary nucleation step in the fibrillization of Aβ, while having little effect on the primary nucleation pathway. Furthermore, binding of sTREM2 to fibrils markedly enhanced uptake of fibrils into human microglial and neuroglioma derived cell lines. The disease-associated sTREM2 mutant, R47H, displayed little to no effect on fibril nucleation and binding, but it decreased uptake and functional responses markedly. We also probed the structure of the WT sTREM2–Aβ fibril complex using integrative molecular modeling based primarily on the cross-linking mass spectrometry data. The model shows that sTREM2 binds fibrils along one face of the structure, leaving a second, mutation-sensitive site free to mediate cellular binding and uptake.

Alzheimer’s disease (AD) is the most common form of dementia and features the neuropathological hallmarks of extracellular Aβ plaques and intraneuronal tau neurofibrillary tangles (1, 2). Human genetic studies on heritable mutations in APP and PSEN causing early-onset familial AD (3) argue that pathogenic Aβ drives tau neurofibrillary tangle formation; in contrast, mutations in MAPT do not lead to Aβ pathology nor cause AD, but rather a rare genetic form of early-onset primary tauopathy (4). In support of the molecular genetics, a recent cross-sectional study in postmortem human AD brain samples demonstrated the presence and correlation of robust prion bioactivity for Aβ and tau proteins in nearly all cases (5), suggesting that even at death, Aβ in prion conformations are active in the late stages of disease. Together, these data establish the importance of pathogenic Aβ throughout AD progression and highlight the urgent need to better understand the cellular and molecular mechanisms that mitigate Aβ’s role in pathogenesis.Microglia are the innate immune effector cell in the brain with myriad functions in healthy aging and neurological diseases. Recent human genetic studies have discovered mutations in several genes encoding microglia-specific proteins that increase risk for AD, thus supporting the notion that microglia are central to AD pathogenesis. Genetic variants of triggering receptor expressed on myeloid cells 2 (TREM2), a cell-surface receptor expressed on myeloid cells and microglia, increase the risk of AD by threefold, implicating microglia and the innate immune system as important determinants in AD pathogenesis (6). TREM2 consists of an extracellular Ig-like domain, a transmembrane domain, and a cytoplasmic tail. Proteolytic cleavage of TREM2 at His157 releases soluble TREM2 (sTREM2) that can be detected in the cerebrospinal fluid (7). While the function of sTREM2 is uncertain, it is believed to promote microglia survival, proliferation, and phagocytosis, making it important for cell viability and innate immune functions in the brain (6, 8, 9). Full-length membrane-bound TREM2 binds to its adaptor protein, DAP12, on the surface of microglia to transmit downstream signaling in response to clustering induced by multivalent ligands (10). Most of the studied mutations are in the Ig-like domain of TREM2. Misfolding, retention, and aberrant shedding are postulated to be caused by some mutations, while other variants have altered ability to interact with their binding partners (8, 11, 12).The R47H mutation in TREM2 constitutes one of the strongest single allele genetic risk factors for AD. The R62H, D87N, and T96K mutations in TREM2 were also linked to AD after extensive analyses of TREM2 polymorphisms (13–16). Several in vivo studies show that TREM2 regulates polarization of microglial processes toward Aβ deposits, leading to plaque compaction and pacification in human AD brain samples and mouse models (17–19). Genetic deletion of TREM2 expression in transgenic mice injected with exogenous Aβ fibrils leads to accelerated amyloid plaque seeding (20). The prominent phenotype in plaque-associated microglia suggests that the effects of AD-risk mutations or genetic deletions are driven by loss of full-length TREM2 signaling. However, a recent in vivo study using exogenously injected recombinant sTREM2 showed reduced amyloid burden and behavioral rescue in mice (21). New clues for the potential importance of sTREM2 in AD have been revealed in clinical studies on living AD patients. sTREM2 can be measured in the cerebrospinal fluid (CSF) and it increases during early stages of AD symptomology (22, 23), suggesting that sTREM2 may be a biomarker for microglia activation. Recent studies indicate that AD patients with relatively high levels of sTREM2 in the CSF have slower rates of amyloid accumulation and reduced cognitive decline (24, 25). These human data support the hypothesis that microglia and sTREM2 play a protective role in early stages of AD progression.While most risk variants of TREM2 exist in the ligand-binding Ig-like domain, the AD-associated point mutation H157Y falls within the stalk region and is known to increase the shedding of full-length TREM2, which possibly results in higher titers of sTREM2 (6). Elevated ectodomain shedding reduces cell-surface full-length TREM2 available for TREM2-mediated phagocytosis and plaque compaction as well as down-stream signal transduction. Although more work is needed, such data begin to suggest there is a delicate balance between the functions of membrane-bound and secreted TREM2, and hence opposing cellular effects of TREM2 variants can emerge (i.e., reduced versus enhanced shedding, which result in similar phenotypic outcomes by reducing cell-surface TREM2) (6, 26).sTREM2 binds to diverse ligands, including phospholipids, apolipoproteins, DNA, and Aβ. Although the full physiological and pathological roles of these interactions remain to be revealed (11, 12, 27, 28), there is general agreement that the extracellular domain of TREM2 (sTREM2) binds to oligomeric forms of Aβ42. However, the observed apparent affinities vary over many orders-of-magnitude (7, 29–31). Most studies were conducted with dimeric Fc fusion proteins, tetrameric constructs, or biotinylated protein bound to the tetrameric streptavidin, which might artificially increase the avidity of the protein for oligomeric forms of Aβ peptides (7, 29–31). Moreover, the studies that report the highest affinities relied on biolayer interferometry or surface plasmon resonance, in which oligomeric protein constructs were immobilized on a surface and Aβ peptides were allowed to diffuse over the surface. Aβ oligomers were found to bind, but they either did not dissociate at all, or they dissociated slowly, leading to affinity estimates in the picomolar to nanomolar range (7, 30, 31). However, the extent of binding of Aβ to the surface did not saturate at concentrations that were orders-of-magnitude greater than the reported dissociation constants, suggesting that the slow off-rate was instead due to precipitation of insoluble Aβ on the bilayer surface (7). In another study, Aβ was fused to the dimeric protein glutathione S-transferase (29). Furthermore, there is inconsistency in the studies involving monomeric Aβ42, with some studies finding nanomolar to low micromolar dissociation constants for the interaction of monomeric Aβ42 and TREM2 ectodomain (29, 30), in contrast to two other studies that reported weak or no interaction (7, 31).To help elucidate the role of sTREM2 and its interaction with Aβ, we evaluated the binding of sTREM2, without any nonnative oligomerization domains added to the studied construct, to specific forms of Aβ40 and Aβ42. We used NMR to show that sTREM2 does not bind to monomeric Aβ, even at high micromolar concentrations. Next, we examined the binding of sTREM2 to fibrils, formed under well-defined conditions to provide a relatively homogenous structure, as assessed by solid-state NMR (32). Additionally, because oligomeric forms of Aβ are heterogeneous and kinetically labile, we opted to determine how sTREM2 affects the formation of intermediates in the fibrillization of Aβ and show that it has a profound effect on the secondary nucleation step of the process. We find that the R47H variant binds to Aβ40 and Aβ42 fibrils with a similar affinity and inhibits their fibrilization just as the WT sTREM2 does. Finally, we show that WT sTREM2, but not the mutant R47H, strongly enhances the uptake of Aβ fibrils in human neural and microglial cells.A second goal of this report was to define the structural underpinnings of the interaction between sTREM2 and Aβ fibrils. Although individual structures of sTREM2 and Aβ40 fibrils have been reported (8, 33), the structures of the complex are not available. The molecular surface of sTREM2 is particularly interesting with regards to its function (8, 29). The crystal structure of the ectodomain of TREM2 (TREM2_ECD) revealed an immunoglobulin fold motif with a highly asymmetric distribution of charged and hydrophobic residues. The surface of the hydrophobic and aromatic protrusion at the top of the structure (Fig. 1, red dotted area) has a highly positive electrostatic potential adjacent to it is a relatively flat surface of positively charged residues (Fig. 1, black dotted area, surface 1). Surface 1 appears suited for binding to acidic moieties (like in Protein Data Bank [PDB] ID code 6B8O) (8). R47 lies near the basic patch, consistent with the R47H mutation disrupting the conformation of the CD loop (8), which comprises a large portion of surface 1. Molecular dynamics simulations suggest that disease-promoting mutations disrupt the apolar character and electrostatic surface of this region of the protein (34). The R47H mutation is also known to disrupt sTREM2’s ability to bind to and signal in response to acidic phospholipids (29). Thus, the data indicate that this surface is important for binding or signaling in response to anionic lipids. In contrast, the determinants of binding to Aβ peptides are uncertain, with different studies coming to differing conclusions concerning the effect of AD mutants on binding or uptake of Aβ fibrils (7, 29–31). Recently, it was suggested that different surfaces might be involved in binding different TREM2 ligands (29). Indeed, sTREM2 has a second unusual, variegated electrostatic surface (surface 2 in Fig. 1), with an extended band of positively charged residues flanked by acidic patches near the top and bottom of the structure, which might interact with different binding partners. Here, we use integrative structural modeling guided by chemical cross-linking mass spectrometry (XL-MS) to map the structure of the fibrillar Aβ–sTREM2 complex, and how it is affected by the R47H substitution. The resulting model suggests that the patch of hydrophobic and basic residues on sTREM2 that contains R47 does not directly interact with Aβ40 fibrils. Instead, sTREM2 is predicted to interact with Aβ primarily via surface 2, while projecting surface 1 away from the amyloid fibrils, with implications for both cellular uptake and signaling.Open in a separate windowFig. 1.Crystal structure of sTREM2 (PDB ID code 5UD7) (8), showing electrostatic potential map of the ectodomain. The white, red, and blue colors in the map correspond to the neutral, acidic, and basic residues, respectively. The map was generated using CHIMERA v1.14 (69). The hydrophobic and aromatic protrusion in sTREM2 is highlighted with a red dashed curve (hydrophobic tip). The flat surface of basic residues adjacent to the hydrophobic tip is shown with black dashed curve (surface 1). Another patch of basic residues, opposite to surface 1, is highlighted with a yellow dashed curve (surface 2). Key residues in these three regions are indicated.     

Histogram analysis of MR imaging-derived cerebral blood volume maps： combined glioma grading and identification of low-grade oligodendroglial subtypes

BACKGROUND AND PURPOSE： Inclusion of oligodendroglial tumors may confound the utility of MR based glioma grading. Our aim was, first, to assess retrospectively whether a histogram-analysis method of MR peifusion images may both grade gliomas and differentiate between low-grade oligodendroglial tumors with or without loss of heterozygosity （LOH） on 1p/19q and, second, to assess retrospectively whether low-grade oligodendroglial subtypes can be identified in a population of patients with high-grade and low-grade astrocytic and oligodendroglial tumors.     

Sequence determinants of the energetics of folding of a transmembrane four-helix-bundle protein

Although previous studies are beginning to point to the specific types of helix-helix interactions that stabilize the folds of membrane-bound helical proteins, quantitative thermodynamic data on natural membrane proteins has been very limited. Here the database is expanded substantially by adding thermodynamic data for a series of sequence variants of M2 protein from influenza A virus. The M2 protein has a single transmembrane helix that homotetramerizes to form proton-selective channels that are essential to virus function. To determine the contributions of specific residues to the folding of this protein, a series of transmembrane peptides with single-site changes near the core of the protein were studied by using sedimentation equilibrium analytical ultracentrifugation. Remarkably, a large number of the mutations increased the stability of the protein. The free energies of tetramerization of the variants can be understood in terms of current models for the structure of the protein. In general, the energetic consequences of the mutations are smaller than those observed for similar mutations in water-soluble proteins. This observation is consistent with previous studies and hence may represent a general phenomenon.