| 1. |
- Abbas, Muhammad Tahir, et al.
(författare)
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Guidelines for an Energy Efficient Tuning of the NB-IoT Stack
- 2020
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Ingår i: 45th IEEE Conference on Local Computer Networks (LCN). - : IEEE Communications Society. ; , s. 60-69
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Konferensbidrag (refereegranskat)abstract
- In this paper, we study the energy consumptionof Narrowband IoT devices. The paper suggests that key tosaving energy for NB-IoT devices is the usage of full Discontinuous Reception (DRX), including the use of connected-mode DRX (cDRX): In some cases, cDRX reduced the energy consumption over a 10-year period with as much as 50%. However, the paper also suggests that tunable parameters, such as the inactivity timer, do have a significant impact. On the basis of our findings, guidelines are provided on how to tune the NB-IoT device so that it meets the target of the 3GPP, i.e., a 5-Wh battery should last for at least 10 years. It is further evident from our results that the energy consumption is largely dependent on the intensity and burstiness of the traffic, and thus could be significantly reduced if data is sent in bursts with less intensity,irrespective of cDRX support.
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| 2. |
- Ahlberg Gagnér, Viktor, 1989, et al.
(författare)
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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments. © 2019, The Author(s).
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| 3. |
- Ahlberg Gagnér, Viktor, et al.
(författare)
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Estimating the probability of coincidental similarity between atomic displacement parameters with machine learning
- 2021
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Ingår i: Machine Learning-Science and Technology. - : IOP Publishing. - 2632-2153. ; 2:3
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution diffraction studies of macromolecules incorporate the tensor form of the anisotropic displacement parameter (ADP) of atoms from their mean position. The comparison of these parameters requires a statistical framework that can handle the experimental and modeling errors linked to structure determination. Here, a Bayesian machine learning model is introduced that approximates ADPs with the random Wishart distribution. This model allows for the comparison of random samples from a distribution that is trained on experimental structures. The comparison revealed that the experimental similarity between atoms is larger than predicted by the random model for a substantial fraction of the comparisons. Different metrics between ADPs were evaluated and categorized based on how useful they are at detecting non-accidental similarity and whether they can be replaced by other metrics. The most complementary comparisons were provided by Euclidean, Riemann and Wasserstein metrics. The analysis of ADP similarity and the positional distance of atoms in bovine trypsin revealed a set of atoms with striking ADP similarity over a long physical distance, and generally the physical distance between atoms and their ADP similarity do not correlate strongly. A substantial fraction of long- and short-range ADP similarities does not form by coincidence and are reproducibly observed in different crystal structures of the same protein.
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| 4. |
- Andersson, Karin, 1972, et al.
(författare)
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Survivin co-ordinates formation of follicular T-cells acting in synergy with Bcl-6
- 2015
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Ingår i: Oncotarget. - : Impact Journals, LLC. - 1949-2553. ; 6:24, s. 20043-20057
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Tidskriftsartikel (refereegranskat)abstract
- Follicular T helper (Tfh) cells are recognized by the expression of CXCR5 and the transcriptional regulator Bcl-6. Tfh cells control B cell maturation and antibody production, and if deregulated, may lead to autoimmunity. Here, we study the role of the proto-oncogene survivin in the formation of Tfh cells. We show that blood Tfh cells of patients with the autoimmune condition rheumatoid arthritis, have intracellular expression of survivin. Survivin was co-localized with Bcl-6 in the nuclei of CXCR5(+)CD4 lymphocytes and was immunoprecipitated with the Bcl-6 responsive element of the target genes. Inhibition of survivin in arthritic mice led to the reduction of CXCR5(+) Tfh cells and to low production of autoantibodies. Exposure to survivin activated STAT3 and induced enrichment of PD-1(+)Bcl-6(+) subset within Tfh cells. Collectively, our study demonstrates that survivin belongs to the Tfh cell phenotype and ensures their optimal function by regulating transcriptional activity of Bcl-6.
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| 5. |
- Andersson, Magnus, et al.
(författare)
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Structural Dynamics of Light-Driven Proton Pumps
- 2009
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Ingår i: Structure. - : Elsevier BV. - 0969-2126 .- 1878-4186. ; 17:9, s. 1265-1275
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Tidskriftsartikel (refereegranskat)abstract
- Bacteriorhodopsin and proteorhodopsin are simple heptahelical proton pumps containing a retinal chromophore covalently bound to helix G via a protonated Schiff base. Following the absorption of a photon, all-trans retinal is isomerized to a 13-cis conformation, initiating a sequence of conformational changes driving vectorial proton transport. In this study we apply time-resolved wide-angle X-ray scattering to visualize in real time the helical motions associated with proton pumping by bacteriorhodopsin and proteorhodopsin. Our results establish that three conformational states are required to describe their photocycles. Significant motions of the cytoplasmic half of helix F and the extracellular half of helix C are observed prior to the primary proton transfer event, which increase in amplitude following proton transfer. These results both simplify the structural description to emerge from intermediate trapping studies of bacteriorhodopsin and reveal shared dynamical principles for proton pumping.
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| 6. |
- Arnlund, David, et al.
(författare)
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Visualizing a protein quake with time-resolved X-ray scattering at a free-electron laser
- 2014
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Ingår i: Nature Methods. - : Springer Science and Business Media LLC. - 1548-7091 .- 1548-7105. ; 11:9, s. 923-926
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Tidskriftsartikel (refereegranskat)abstract
- We describe a method to measure ultrafast protein structural changes using time-resolved wide-angle X-ray scattering at an X-ray free-electron laser. We demonstrated this approach using multiphoton excitation of the Blastochloris viridis photosynthetic reaction center, observing an ultrafast global conformational change that arises within picoseconds and precedes the propagation of heat through the protein. This provides direct structural evidence for a 'protein quake': the hypothesis that proteins rapidly dissipate energy through quake-like structural motions.
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| 7. |
- Bodor, Andrea, et al.
(författare)
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DYNLL2 Dynein Light Chain Binds to an Extended Linear Motif of Myosin 5a Tail That Has Structural Plasticity.
- 2014
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 1520-4995 .- 0006-2960. ; 53:45, s. 7107-7122
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Tidskriftsartikel (refereegranskat)abstract
- LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a β-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the β-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif.
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| 8. |
- Bourgeois, Dominique, et al.
(författare)
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Raman-assisted X-ray crystallography for the analysis of biomolecules.
- 2009
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Ingår i: Methods in molecular biology (Clifton, N.J.). - Totowa, NJ : Humana Press. - 1064-3745. ; 544, s. 253-67
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Tidskriftsartikel (refereegranskat)abstract
- In this chapter, we describe Raman microspectrophotometry applied to crystals of biomolecules. Raman spectra collected in crystallo provide structural information highly complementary to X-ray diffraction, relate the crystalline state to the solution state, and allow the identification of ligand-bound or intermediate states of macromolecules. Nonresonant Raman spectroscopy is particularly suitable to the study of macromolecular crystals, and therefore applies to a wide range of noncolored crystalline proteins. Practical issues related to the investigation of crystals by Raman microspectrophotometry are reviewed, and the current limitations are highlighted.
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| 9. |
- Boutet, S., et al.
(författare)
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High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography
- 2012
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 337:6092, s. 362-364
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Tidskriftsartikel (refereegranskat)abstract
- Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.
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| 10. |
- Burgess, Selena G, et al.
(författare)
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Probing the dynamic interface between trimethylamine dehydrogenase (TMADH) and electron transferring flavoprotein (ETF) in the TMADH—2ETF complex: role of the Arg-alpha237 (ETF) and Tyr-442 (TMADH) residue pair.
- 2008
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 47:18, s. 5168-5181
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Tidskriftsartikel (refereegranskat)abstract
- We have used multiple solution state techniques and crystallographic analysis to investigate the importance of a putative transient interaction formed between Arg-alpha237 in electron transferring flavoprotein (ETF) and Tyr-442 in trimethylamine dehydrogenase (TMADH) in complex assembly, electron transfer, and structural imprinting of ETF by TMADH. We have isolated four mutant forms of ETF altered in the identity of the residue at position 237 (alphaR237A, alphaR237K, alphaR237C, and alphaR237E) and with each form studied electron transfer from TMADH to ETF, investigated the reduction potentials of the bound ETF cofactor, and analyzed complex formation. We show that mutation of Arg-alpha237 substantially destabilizes the semiquinone couple of the bound FAD and impedes electron transfer from TMADH to ETF. Crystallographic structures of the mutant ETF proteins indicate that mutation does not perturb the overall structure of ETF, but leads to disruption of an electrostatic network at an ETF domain boundary that likely affects the dynamic properties of ETF in the crystal and in solution. We show that Arg-alpha237 is required for TMADH to structurally imprint the as-purified semiquinone form of wild-type ETF and that the ability of TMADH to facilitate this structural reorganization is lost following (i) redox cycling of ETF, or simple conversion to the oxidized form, and (ii) mutagenesis of Arg-alpha237. We discuss this result in light of recent apparent conflict in the literature relating to the structural imprinting of wild-type ETF. Our studies support a mechanism of electron transfer by conformational sampling as advanced from our previous analysis of the crystal structure of the TMADH-2ETF complex [Leys, D. , Basran, J. , Sutcliffe, M. J., and Scrutton, N. S. (2003) Nature Struct. Biol. 10, 219-225] and point to a key role for the Tyr-442 (TMADH) and Arg-alpha237 (ETF) residue pair in transiently stabilizing productive electron transfer configurations. Our work also points to the importance of Arg-alpha237 in controlling the thermodynamics of electron transfer, the dynamics of ETF, and the protection of reducing equivalents following disassembly of the TMADH-2ETF complex.
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