Entire Helix Research Articles

Cognitive Soil Digital Twin for Monitoring the Soil Ecosystem: A Conceptual Framework

The digital twin concept has found widespread application across diverse industries. Herein, we present a comprehensive conceptual framework for the cognitive soil digital twin, which embodies the intricate physical reality of the soil ecosystem, aiding in its holistic monitoring and comprehension. The digital twin can seamlessly integrate a multitude of sensor data sources, including field Internet of Things sensors, remote sensing data, field measurements, digital cartography, surveys, and other Earth observation datasets. By virtue of its duality, this digital counterpart facilitates data organisation and rigorous analytical exploration, unravelling the intricacies of physical, chemical, and biological soil constituents while discerning their intricate interrelationships and their impact on ecosystem services. Its potential extends beyond mere data representation, acting as a versatile tool for scenario analysis and enabling the visualisation of diverse environmental impacts, including the effects of climate change and transformations in land use or management practices. Beyond academic circles, the digital twin’s utility extends to a broad spectrum of stakeholders across the entire quadruple helix, encompassing farmers and agronomists, soil researchers, the agro-industry, and policy-makers. By fostering collaboration among these stakeholders, the digital twin catalyses informed decision-making, underpinned by data-driven insights. Moreover, it acts as a testbed for the development of innovative sensors and monitoring frameworks, in addition to providing a platform that can educate users and the broader public using immersive and innovative visualisation tools, such as augmented reality. This innovative framework underscores the imperative of a holistic approach to soil ecosystem monitoring and management, propelling the soil science discipline into an era of unprecedented data integration and predictive modelling, by harnessing the effects of climate change towards the development of efficient decision-making.

Deep learning based automatic Debakey classification of aortic dissection using CT plain scan

ObjectiveThis paper presents an automatic segmentation and classification of aortic dissection by utilizing neural network based on CT scanning. MethodologyFirst we present a way of establishing models of indivisible aorta parametrization, designed multiple seed points as the initial parameter and based on the three-dimensional area growth algorithm, finally add morphological processing to realize the segmentation of inner membrane, and then introduced the semantic segmentation framework, and analyzed the characteristics and function of each part, improve the Deeplabv3 + network. This paper analyzes the results of the different experiments with two-dimensional lattices and presents the advantages of being sensitive to differences in shape and position and of not being able to use three-dimensional spatial continuity. Our research establishs the aorta reconstruction, which is simpler for learning the transformation of both the shape and position of, according to a last for three-dimensional CT images interfloor of the entire helix network aorta 3D MPRNet.A new module of multi-scale receptive field information fusion is designed, which realizes the function of acquiring different receptive field features, taking into account details and global features, so that the model obtains the unique ability more suitable for segmentation problems. In the decoder stage, the cross-layer connection mode similar to U-Net is still adopted to realize the fusion of semantic information at high and low levels, which ensures that the network can learn enough features. ResultsThe full convolutional network and traditional algorithms based on domain knowledge of aortic dissection images achieve a robust, automated and high precision CT image aortic dissection segmentation scheme. ConclusionThe large number of decoder parameters is increased, which increases the difficulty of network training and reduces the reasoning speed of the model. At the same time, not all features are useful information, while the high frequency and low frequency, the feature graph only adopts cross-layer connection to connect shallow features to high-level information may bring the redundancy of information and interference with useful information. Therefore, designing an efficient decoder is another research idea to accelerate model inference and improve segmentation accuracy.

Dynamics transitions of the KvAP voltage sensor during lipid-dependent gating.

In response to changes in membrane potential, the S4 helix of VSD undergoes a structural transition from resting/‘Down’ to activated/‘Up’ conformation, which is an extremely important step for the functioning of a voltage-gated ion channel. It is well known that the presence of phospholipid headgroups are an absolute requirement for the normal functioning of Kv channels whereas channels reconstituted in lipids lacking the phosphate headgroups renders the channel nonfunctional. Interestingly, apart from voltage-dependent gating, the gating of KvAP can also be influenced by the change in membrane lipid composition in a voltage-independent manner (i.e., lipid-dependent gating). Here, we have performed differential lipid reconstitution using liposomes composed of phospholipids (POPC/POPG) to stabilize the activated/‘Up’ conformation and using liposomes with a mixture of phospholipids and non-phospholipids (DOPC/cholesterol) to trap the isolated KvAP-VSD in its ‘Down’ conformation. The results, using site-directed NBD fluorescence on the entire S4 helix, show that the moving part of the KvAP sensor adopts a relaxed dynamics in its ‘Down’ state whereas a restricted dynamics is observed in its ‘Up’ state. Further, a variation in hydration dynamics is observed when the S4 transitions between the two functional states, which not only reduces the relative discrete population of S4 conformations, but also alters the lifetime distribution peaks of the S4 in ‘Down’ conformation. This strongly suggests that the structural dynamics and conformational heterogeneity of the S4 is significantly altered which correlates with the change in conformation of the sensor during gating in membranes. Importantly, our ‘Down’ state results strongly indicate a bending/breakage from the middle of the otherwise straight S4-helix in ‘Up’ conformation. Overall, our results highlight the impact of altered lipid-protein interface that has a strong influence on the structural dynamics of the functionally-important conformations of the KvAP sensor.

CryoET structures of immature HIV Gag reveal six-helix bundle

Gag is the HIV structural precursor protein which is cleaved by viral protease to produce mature infectious viruses. Gag is a polyprotein composed of MA (matrix), CA (capsid), SP1, NC (nucleocapsid), SP2 and p6 domains. SP1, together with the last eight residues of CA, have been hypothesized to form a six-helix bundle responsible for the higher-order multimerization of Gag necessary for HIV particle assembly. However, the structure of the complete six-helix bundle has been elusive. Here, we determined the structures of both Gag in vitro assemblies and Gag viral-like particles (VLPs) to 4.2 Å and 4.5 Å resolutions using cryo-electron tomography and subtomogram averaging by emClarity. A single amino acid mutation (T8I) in SP1 stabilizes the six-helix bundle, allowing to discern the entire CA-SP1 helix connecting to the NC domain. These structures provide a blueprint for future development of small molecule inhibitors that can lock SP1 in a stable helical conformation, interfere with virus maturation, and thus block HIV-1 infection.

Accurate and Efficient Thermal Analysis of Slow Wave Structures for Helix Traveling-Wave Tubes by Finite-Element Method

In slow wave structures (SWSs) for helix traveling-wave tubes, both thermal conductivities (TCs) of materials and thermal contact resistances (TCRs) are temperature-dependent, which have a great influence on the heat dissipation of helix SWSs. This article presents an accurate and efficient thermal analysis method of helix SWSs by finite-element method (FEM). In this method, a novel contact boundary condition (CBC) approach is proposed. This CBC approach can easily integrate various TCR models to simulate temperature-dependent TCRs accurately and conveniently. Specially for double nonlinearities arising from temperature-dependent TCs and TCRs within helix SWSs, a fast nonlinear solver named FMONS is also proposed to significantly improve the efficiency of the thermal simulation for helix SWSs. Based on this method, we further developed a 3-D thermal design tool for helix SWSs called TS2. Different from all the present FEM codes, for example, ANSYS, our TS2 can directly model temperature-dependent TCRs. By simulating various helix SWSs including a global model of the entire helix SWS, it is found that our TS2 has very high accuracy and efficiency in the thermal analysis of helix SWSs, which would be very useful for the design of high-power helix traveling-wave tubes.

Calmodulin binds to Drosophila TRP with an unexpected mode

Drosophila TRP is a calcium-permeable cation channel essential for fly visual signal transduction. During phototransduction, Ca2+ mediates both positive and negative feedback regulation on TRP channel activity, possibly via binding to calmodulin (CaM). However, the molecular mechanism underlying Ca2+ modulated CaM/TRP interaction is poorly understood. Here, we discover an unexpected, Ca2+-dependent binding mode between CaM and TRP. The TRP tail contains two CaM binding sites (CBS1 and CBS2) separated by an ∼70-residue linker. CBS1 binds to the CaM N-lobe and CBS2 recognizes the CaM C-lobe. Structural studies reveal the lobe-specific binding of CaM to CBS1&2. Mutations introduced in both CBS1 and CBS2 eliminated CaM binding in full-length TRP, but surprisingly had no effect on the response to light under physiological conditions, suggesting alternative mechanisms governing Ca2+-mediated feedback on the channel activity. Finally, we discover that TRPC4, the closest mammalian paralog of Drosophila TRP, adopts a similar CaM binding mode.

Optical Forces Acting on a Double DNA-Like Helix, Its Unwinding and Strands Rupture

In this paper we study electromagnetic forces induced on DNA and DNA-like helices by external electromagnetic waves. We consider simultaneously occurring forces and torques, interconnected and acting along the double helix axis. Since the DNA molecule has an absorption band in the ultraviolet and visible range near wavelengths λ1res=280 nm and λ2res=500 nm, we expect that it may be possible to selectively apply engineered forces to DNA molecules using appropriate illumination by light in these frequency ranges. The optical forces are simulated for DNA fragments consisting of 20 and 35 turns. Fragments of this length are convenient for direct sequencing and subsequent use in experiments and in practice. It is shown that repulsion forces can arise between the strands of the double DNA-like helix in the field of external electromagnetic waves. Such forces are characteristic of a DNA-like helix with its specific pitch angle and are not inherent in double helices with more straightened or more compressed turns. These repulsion forces, acting along the entire helix, both for electric charges and for electric currents, can lead to damage and rupture of the strands in the double helix. In addition, there can also exist forces and moments of forces directed along the helix axis, which simultaneously stretch and unwind a double helix. The double helix equilibrium under the action of optical forces is also of interest from another point of view, i.e., for optimizing the structure of artificial magnetics and bianisotropic metamaterials for applications in all frequency ranges.

Self-Assembly of N-Terminal Aryl Amino Acids into Adaptive Single- and Double-Strand Helices.

Helical structures are important features of many important biomacromolecules such as double helices and single α-helices in DNA and protein, respectively, yet the self-organization of short oligopeptides (<3) or independent amino acids into artificial helical structures on the atomic level remains mysterious. Here we present the direct construction of artificial double and single helices from N-terminated aryl amino acids (ferrocene phenylalanine (Phe) conjugates) despite both Phe and Phe-Phe dipeptide self-aggregations adopting supramolecular β-sheet structures, which also demonstrated chirality evolution exposed to small molecular binders. In the solid state, the box-shaped building unit stacks into a double helix with enantiomer-resolved handedness driven orthogonally by H-bonds and the CH-π interaction. The entire double helix is noncovalently linked except for the hybridization regions. Asymmetric H-bonds between carboxylic acids and amides facilitates the one-dimensional helical packing of amino acid residues. The ditopic building unit adopts intramolecular H-bonds, facilitating single-strand helix formation. In aqueous self-assemblies, the superhelical structures were retained, which underwent chirality transfer and handedness inversion upon complexation orthogonally by H-bonds and charge-transfer interaction, showing adaptivity to environmental factors.

Exploring the structural origins of cryptic sites on proteins

Molecular dynamics (MD) simulations of proteins reveal the existence of many transient surface pockets; however, the factors determining what small subset of these represent druggable or functionally relevant ligand binding sites, called "cryptic sites," are not understood. Here, we examine multiple X-ray structures for a set of proteins with validated cryptic sites, using the computational hot spot identification tool FTMap. The results show that cryptic sites in ligand-free structures generally have a strong binding energy hot spot very close by. As expected, regions around cryptic sites exhibit above-average flexibility, and close to 50% of the proteins studied here have unbound structures that could accommodate the ligand without clashes. Nevertheless, the strong hot spot neighboring each cryptic site is almost always exploited by the bound ligand, suggesting that binding may frequently involve an induced fit component. We additionally evaluated the structural basis for cryptic site formation, by comparing unbound to bound structures. Cryptic sites are most frequently occluded in the unbound structure by intrusion of loops (22.5%), side chains (19.4%), or in some cases entire helices (5.4%), but motions that create sites that are too open can also eliminate pockets (19.4%). The flexibility of cryptic sites frequently leads to missing side chains or loops (12%) that are particularly evident in low resolution crystal structures. An interesting observation is that cryptic sites formed solely by the movement of side chains, or of backbone segments with fewer than five residues, result only in low affinity binding sites with limited use for drug discovery.

The Significance of Surface Complementarity on the Free Energy of Membrane Protein Assembly in Membranes

The dimerization interface of the 18-TM helix ClC-ec1 Cl-/H+ antiporter is formed by four alpha helices (H, I, P and Q) that are lined entirely by non-polar residues (leucines and isoleucines). The resultant surface fits well with its protein partner, presenting ClC-ec1 as an interesting model system to study the effect of shape complementarity on the stability of protein association. Recently, we established single-molecule fluorescence microscopy methods allowing for the measurement of the equilibrium dimerization reaction of ClC-ec1 in 2:1 POPE/POPG lipid bilayers. Here, we investigate the effect that cavities, engineered via subtractive substitutions to ALA, have on the free energy of dimerization in the lipid bilayer. We first engineered ClC constructs with large cavities by mutating entire helix surfaces to ALA, 4-5 residues at a time. Each of these constructs were stable and folded upon purification in detergent, and demonstrated comparable functional Cl- transport after reconstitution in membranes. However, while all-ALA helix I, P and Q are almost entirely dimeric as determined by size exclusion chromatography in detergent, all-ALA helix H shifts to a monomeric form. Further investigation of the residues on helix H indicates that L194A alone is responsible for the shift to the monomeric state. Cysteine accessibility and functional reconstitution experiments show that L194A is folded and functional in both monomeric and dimeric states. Measurement of the ΔΔG of dimerization in 2:1 POPE/POPG shows that L194A shifts stability by 2 kcal/mole, similar to the effect of a bulky I422W substitution at the interface. We conclude that L194 is an energetic hotspot on the dimerization interface, but the reason for this shift in stability remains unknown. Examination of the structure shows that L194 is positioned along the symmetry interface of the subunit fold suggesting that it may be involved in defining the shape of the dimerization interface, and thus mutation may alter shape complementarity by increasing dynamics of those helices.

Quantitative Chemical Imaging of Nonplanar Microfluidics.

Confocal and multiphoton optical imaging techniques have been powerful tools for evaluating the performance of and monitoring experiments within microfluidic devices, but this application suffers from two pitfalls. The first is that obtaining the necessary imaging contrast often requires the introduction of an optical label which can potentially change the behavior of the system. The emerging analytical technique stimulated Raman scattering (SRS) microscopy promises a solution, as it can rapidly measure 3D concentration maps based on vibrational spectra, label-free; however, when using any optical imaging technique, including SRS, there is an additional problem of optical aberration due to refractive index mismatch between the fluid and the device walls. New approaches such as 3D printing are extending the range of materials from which microfluidic devices can be fabricated; thus, the problem of aberration can be obviated simply by selecting a chip material that matches the refractive index of the desired fluid. To demonstrate complete chemical imaging of a geometrically complex device, we first use sacrificial molding of a freeform 3D printed template to create a round-channel, 3D helical micromixer in a low-refractive-index polymer. We then use SRS to image the mixing of aqueous glucose and salt solutions throughout the entire helix volume. This fabrication approach enables truly nonperturbative 3D chemical imaging with low aberration, and the concentration profiles measured within the device agree closely with numerical simulations.

Die Helix in der Ohrakupunktur

The auricle is the most famous micro system in the western world, first described by Paul Nogier [1]. The therapy of neuralgic grievances by means of ear-acupuncture has not been very effective in the past. This may well be due to the fact that classical textbooks on ear-acupuncture [e. g. 2, 3] had described and restricted the area of „sensitive segmental nerve roots”, appropriate for neuralgic purposes, to the helix descendens from Darwin Point down to the bottom of the helix [2, 3]. However, needling of the helix for neuralgic pain will be significantly more effective by using the entire helix from its root – corresponding to the foot area – until its lower end – addressing the Nervus auricularis – and further down on the outer rim of the Lobulus addressing Nervus trigeminus [4–8]. Allocation of the therapeutic point at the outer rim of helix is best achieved by applying the method of P. Nogier, that is by pattering a radius from “point zero” over the representative point for pain at the auricle, extending to the helix. Mainly situated on the outer rim, one or more activated points are identified, which correlate with the neuralgic pain. In order to specify the exact point I prefer the RAC.

Protein-Backbone Thermodynamics across the Membrane Interface

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Exclusion of small terminase mediated DNA threading models for genome packaging in bacteriophage T4.

Tailed bacteriophages and herpes viruses use powerful molecular machines to package their genomes. The packaging machine consists of three components: portal, motor (large terminase; TerL) and regulator (small terminase; TerS). Portal, a dodecamer, and motor, a pentamer, form two concentric rings at the special five-fold vertex of the icosahedral capsid. Powered by ATPase, the motor ratchets DNA into the capsid through the portal channel. TerS is essential for packaging, particularly for genome recognition, but its mechanism is unknown and controversial. Structures of gear-shaped TerS rings inspired models that invoke DNA threading through the central channel. Here, we report that mutations of basic residues that line phage T4 TerS (gp16) channel do not disrupt DNA binding. Even deletion of the entire channel helix retained DNA binding and produced progeny phage in vivo. On the other hand, large oligomers of TerS (11-mers/12-mers), but not small oligomers (trimers to hexamers), bind DNA. These results suggest that TerS oligomerization creates a large outer surface, which, but not the interior of the channel, is critical for function, probably to wrap viral genome around the ring during packaging initiation. Hence, models involving TerS-mediated DNA threading may be excluded as an essential mechanism for viral genome packaging.

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins.

GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. GemC1 shows a less typical coiled coil compared with the Geminin homodimer and the Geminin-Idas heterodimer structures. It is also shown that both in vitro and in cells GemC1 interacts with Geminin through its coiled-coil domain, forming a heterodimer that is more stable that the GemC1 homodimer. Comparative analysis of the thermal stability of all of the possible superfamily complexes, using circular dichroism to follow the unfolding of the entire helix of the coiled coil, or intrinsic tryptophan fluorescence of a unique conserved N-terminal tryptophan, shows that the unfolding of the coiled coil is likely to take place from the C-terminus towards the N-terminus. It is also shown that homodimers show a single-state unfolding, while heterodimers show a two-state unfolding, suggesting that the dimer first falls apart and the helices then unfold according to the stability of each protein. The findings argue that Geminin-family members form homodimers and heterodimers between them, and this ability is likely to be important for modulating their function in cycling and differentiating cells.

Sequence-dependent binding of flavonoids to duplex DNA.

The whole family of structurally distinct flavonoids has been recognized as a valuable source of prospective anticancer agents. There is experimental evidence demonstrating that some flavonoids, like flavopiridol (FLP) and quercetin (QUE), bind to DNA influencing their key physiological function. FLP is involved in the combined mode of interaction (intercalation and minor groove binding), while QUE is viewed as a minor groove binder. From a physical standpoint, experimental and theoretical studies have not so far provided a sufficiently consistent picture of the nature of interaction with DNA. Herein the sequence-dependent binding of FLP and of QUE (two representative examples of the structurally different flavonoids) with duplex DNA, containing a variety of the sequences of eight nucleotides (I: GGGGCCCC, II: GGCCGGCC, III: AAAATTTT, IV: AAGCGCTT, V: GCGCGCGC) in the 5'-strand, is investigated using a sophisticated molecular dynamics (MD) approach. For various parts (helix, backbone, bases) of the DNA structure, the change of asymptotic (in terms of an infinite length of MD simulation) configurational entropy, being the thermodynamic consequence of DNA flexibility change due to ligand binding, is explored. As far as the sequence-dependent extent of DNA flexibility change upon QUE (or FLP) binding is concerned, for the entire double helix, increased flexibility is observed for I (or I ≈ II), while increased rigidity is found to be in the order of V > III > II > IV (or III > V > IV) for the rest of sequences. For the backbone, increased rigidity in the order of V > III > II > IV > I (or III > V > IV > I > II) is generally observed. For the nucleobases, increased flexibility is determined for I and II (I > II for both ligands), while increased rigidity in the order of V ≈ III > IV (or III > V > IV) is reported for the other sequences. Of the overall increased rigidity of the DNA structure upon ligand binding that is observed for the sequences III, IV, and V, about 50-70% comes from the sugar-phosphate backbone. Noteworthy is that the increased flexibility of the entire double helix and of the complete system of nucleobases upon ligand binding is only established for sequence I. The insights are further subtly substantiated by considering the configurational entropy contributions at the level of individual nucleobase pairs and of individual nucleo-base pair steps and by analyzing the sequence dependent estimates of intra-base pair entropy and inter-base pair entropy. The GGC triplet, which is part of the central tetramer (GGCC) of I, is concluded to be critical for binding of flavonoids, while the effect of the presence of ligand to the flexibility of nucleobases is localized through the intra-base pair motion of the intercalation site and its immediate vicinity. G-rich DNA sequences with consecutive Gs going before and/or after the critical GGC code (such as I: GGGGCCCC) are proposed to be uniquely specific for flavonoids. The configurational entropy contribution, as an upper bound of the true entropy contribution to the free energy in noncovalent binding, is demonstrated to influence the fundamental discrimination (intercalation vs groove binding) of DNA-flavonoid recognition modes. Some interesting implications for the structure-based design of optimal DNA binders are discussed.

Alpha-bulges in G protein-coupled receptors.

Agonist binding is related to a series of motions in G protein-coupled receptors (GPCRs) that result in the separation of transmembrane helices III and VI at their cytosolic ends and subsequent G protein binding. A large number of smaller motions also seem to be associated with activation. Most helices in GPCRs are highly irregular and often contain kinks, with extensive literature already available about the role of prolines in kink formation and the precise function of these kinks. GPCR transmembrane helices also contain many α-bulges. In this article we aim to draw attention to the role of these α-bulges in ligand and G-protein binding, as well as their role in several aspects of the mobility associated with GPCR activation. This mobility includes regularization and translation of helix III in the extracellular direction, a rotation of the entire helix VI, an inward movement of the helices near the extracellular side, and a concerted motion of the cytosolic ends of the helices that makes their orientation appear more circular and that opens up space for the G protein to bind. In several cases, α-bulges either appear or disappear as part of the activation process.

Analysis of Mammalian rDNA Internal Transcribed Spacers

Nuclear rDNA Internal Transcribed Spacers, ITS1 and ITS2, are widely used for eukaryote phylogenetic studies from the ordinal level to the species level, and there is even a database for ITS2 sequences. However, ITS regions have been ignored in mammalian phylogenetic studies, and only a few rodent and ape sequences are represented in GenBank. The reasons for this dearth, and the remedies, are described here. We have recovered these sequences, mostly >1 kb in length, for 36 mammalian species. Sequence alignment and transcript folding comparisons reveal the rRNA transcript secondary structure. Mammalian ITS regions, though quite long, still fold into the recognizable secondary structure of other eukaryotes. The ITS2 in particular bears the four standard helix loops, and loops II and III have the hallmark characters universal to eukaryotes. Both sequence and insertions/deletions of transcript secondary structure helices observed here support the four superorder taxonomy of Placentalia. On the family level, major unique indels, neatly excising entire helices, will be useful when additional species are represented, resulting in significant further understanding of the details of mammalian evolutionary history. Furthermore, the identification of a highly conserved element of ITS1 common to warm-blooded vertebrates may aid in deciphering the complex mechanism of RNA transcript processing. This is the last major group of terrestrial vertebrates for which rRNA ITS secondary structure has been resolved.

Membrane bound α-synuclein is fully embedded in the lipid bilayer while segments with higher flexibility remain

Cellular pathways involving α-synuclein (αS) seem to be causative for development of Parkinson’s disease. Interactions between αS and lipid membranes appear to be important for the physiological function of the protein and influence the pathological aggregation of αS leading to the formation of amyloid plaques. Upon membrane binding the unstructured αS folds into amphipathic helices. In our work we characterized the penetration depth and probed the local environment of Trp-residues introduced along the αS sequence. We could show that while the entire helix is well embedded in the lipid bilayer, segments with a shallower penetration and supposable higher flexibility exist.

Alternative C-Terminal Helix Orientation Alters Chemokine Function: STRUCTURE OF THE ANTI-ANGIOGENIC CHEMOKINE, CXCL4L1

CXCL4L1 is a highly potent anti-angiogenic and anti-tumor chemokine, and its structural information is unknown. CXCL4L1 x-ray structure is determined, and it reveals a previously unrecognized chemokine structure adopting a novel C-terminal helix conformation. The alternative helix conformation enhances the anti-angiogenic activity of CXCL4L1 by reducing the glycosaminoglycan binding ability. Chemokine C-terminal helix orientation is critical in regulating their functions. Chemokines, a subfamily of cytokines, are small, secreted proteins that mediate a variety of biological processes. Various chemokines adopt remarkable conserved tertiary structure comprising an anti-parallel β-sheet core domain followed by a C-terminal helix that packs onto the β-sheet. The conserved structural feature has been considered critical for chemokine function, including binding to cell surface receptor. The recently isolated variant, CXCL4L1, is a homologue of CXCL4 chemokine (or platelet factor 4) with potent anti-angiogenic activity and differed only in three amino acid residues of P58L, K66E, and L67H. In this study we show by x-ray structural determination that CXCL4L1 adopts a previously unrecognized structure at its C terminus. The orientation of the C-terminal helix protrudes into the aqueous space to expose the entire helix. The alternative helix orientation modifies the overall chemokine shape and surface properties. The L67H mutation is mainly responsible for the swing-out effect of the helix, whereas mutations of P58L and K66E only act secondarily. This is the first observation that reports an open conformation of the C-terminal helix in a chemokine. This change leads to a decrease of its glycosaminoglycan binding properties and to an enhancement of its anti-angiogenic and anti-tumor effects. This unique structure is recent in evolution and has allowed CXCL4L1 to gain novel functional properties.