Supplementary material
|
|
- Sabina Caldwell
- 5 years ago
- Views:
Transcription
1 Supplementary material Docking procedures PtdIns(4)P headgroup docked onto FAPP1-PH The ligand structure and charges were generated within GHEMICAL (Hassinen and Perakyla, 2001) using minimization (500 steps, gradient cutoff kcal.mol -1.Å -1 ) semi-empirical method PM3 to generate partial charges. The PH domain was prepared with Autodock Tool (ADT) using the coordinates of the minimized ligand and the lowest energy protein structure to which Kollman charges were added. A grid of 60 3 points with a spacing of Å was centered on of the region exhibiting C 6 - PtdIns(4)P induced perturbations. A distance dependent dielectric constant of was used to calculate the maps. The ligand was subjected to 100 docking runs using the Lamarckian Genetic Algorithm. Cluster analysis was performed using a root mean square (RMS) tolerance of 2 Å and interactions were analyzed with ADT. This yielded three clusters (Table SIV). The most frequently populated cluster positioned the 1-phosphate and attached acyl chains near hydrophobic protrusion to allow parallel insertion. In contrast, the other, symmetry-related clusters reversed the 1- and 4-phosphate positions and were antiparallel, and hence were judged to be physiologically unreasonable. DPC micelles docked onto FAPP1-PH Flexibility was introduced for residues K7-R18, E50, D57 and G67-A75 based on their micelle-induced chemical shift changes and solvent accessibility estimated with NACCESS. The docking protocol began with 400 randomly oriented and spatially separated protein and micelle structures taken from the representative ensembles (Dancea et al., 2008).
2 List of Figures and Tables Figure S1: Electrostatic surfaces of FAPP1-PH calculated with APBS, with the orientation at right being identical to that shown in panels 1B and 1C. Figure S2: Comparison of 1 H, 15 N HSQC spectra of FAPP1-PH with and without inorganic phosphate. Collected at 800 MHz with a protein concentration of 200 μm. Figure S3: Chemical shift perturbations in FAPP1-PH resonances upon lipid titrations followed in 15 N HSQC spectra Figure S4: HSQC spectra of FAPP1-PH showing the intensity reduction of H N protons in presence of doxyl derivatives Figure S5: Membrane sheet tubulation assay with mutant Y11L12-GG and Y11L12- EE GST-FAPP2 versions FigureS6: Chemical shift perturbations in FAPP1-PH resonances upon addition of 1mM PtdIns(3,4)P 2 and PtdIns(4,5)P 2 Figure S7: PtdSer specifically enhances FAPP1-PH binding to micelles containing PtdIns(4)P Figure S8: The diffusion coefficient (D) of a sample containing 200 μm FAPP1-PH Figure S9: The purified wild type and C94S mutant proteins yielded similar 1D 1H NMR spectra Table SI. Statistics for the ensemble of FAPP1-PH domain solution structures Table SII. Structural statistics of the best 20 models of FAPP1-PH/DPC micelles Table SIII. Primers used to generate FAPP2-GST mutants
3 Figure S1: Two views of the electrostatic surface of the representative FAPP1-PH structure calculated with APBS, with the orientation at right being similar to that shown in Figure 2B. Figure S2: FAPP1-PH does not bind phosphate detectably despite its exposed basic surfaces. Comparison of HSQC spectra of the 15 N labeled FAPP1-PH domain (200 μm) in the presence (blue) and absence (red) of 1.5 mm inorganic phosphate reveals no significant interaction.
4 Figure S3: Chemical shift changes induced upon titrations of FAPP1-PH with micelles or ligand, as monitored in 1 H, 15 N HSQC spectra. The CSPs induced by increasing concentrations of DPC/CHAPS micelles (A) or C 6 -PtdIns(4)P (B) to the apo FAPP1-PH, or by C 8 -PtdIns(4)P to a sample containing FAPP1-PH (2000 μm) and DPC/ /CHAPS (4 mm DPC) (C) are shown. Stock solutions of the indicated ligand were added to the 15 N-labelled protein using identical solution conditions. The micelle concentration indicated in (A) assumes 54 DPC molecules per micelle. The normalized CSPs are shown in panels D,E and F, respectively. The red lines correspond to mean ( ) plus standard deviation (σ) (D) or the mean plus two standard deviations (E). The labels indicate the residues with substantially perturbed resonances (i.e. greater than those shown by the red lines) upon addition of ligand. The Trp indole NH signals are labeled with an e. The extensive CSPs induced by C 8 -PtdIns(4)P in the presence of micelles are mapped on FAPP1-PH structure (G),
5 with residues undergoing slow exchange colored in pink. Residues colored in cyan and blue exhibit CSPs over and 0.07, respectively. Asterisks in panels C and E represent Y11 and T23, which exhibit broad and overlapped peaks. Boxed residues are buried in the interior of the protein. Titration points for DPC/CHAPS titrations and c6-ptdins(4)p are shown for residues L12 and Y29, respectively (H).
6 Figure S4: PRE NMR data identifying the buried wedge. The intensity reductions of H N signals of FAPP1-PH induced by adding 14- (A) and 5-doxyl PC (B) into DPC/ /CHAPS micelles was mapped ontoo the FAPP1-PH surface (C). Backbone and sidechain atoms for which the H N signal intensity was significantly reduced upon addition of 14-doxyl to the micelles are indicated as red spheres and traces, respectively, on the ribbon structure (D). The 15 N HSQC spectra of FAPP1-PH mixed with micelles containing equimolar 5-doxyl or 14-doxyl (E) derivative are superimposed with control spectra containing DPPC. Residues whose signal intensities are dramatically reduced by the presence of doxyl derivatives in the micelle are labeled.
7 Figure S5: FAPP2-mediated tubulation of flat membrane sheets requires an intact wedge. Abolishment of tubulation activity of mutant Y11L12-GG and Y11L12-EE forms of a GST fusion of full length human FAPP2 protein on lipid membrane sheets containing POPC:PtdIns(4)P (98:2 mol%) shown by DIC. Previous studies have demonstrated the PtdIns(4)P-dependent membrane tubulation activity of FAPP2 using the same assay conditions (Cao et al, 2009). Screen shots were taken from Movies. Tubulation was initiated by injection of 5 μl FAPP2 (1 mg/ml) into the reaction chamber.
8 Figure S6: Polyphosphorylated PIs bind similarly to the FAPP1-PH. Normalized CSPs induced in 15 N-labelled FAPP1-PH (200 μm) upon addition of submicellar concentrations (1 mm) of C6-PtdIns(3,4 6 )P 2 (top panel) and C 6 -PtdIns(4,5)PP 2 (bottom panel). The 15 N, 1 H HSQC spectra were collected at 800 MHz in the NMR buffer.
9 Figure S7: PtdSer specifically enhances FAPP1-PH binding to micelles containing PtdIns(4)P. The interaction of soluble C 6 6-PtdSer (1.5mM) with the PtdIns(4) )P binding pocket is comparatively weak based on the normalized CSPs induced in 15 N-labelled FAPP1-PH (2000 μm) (top panel). Upon addition of C 6 -PtdSer (80 μm) to the DPC/ /CHAPS complexed FAPP1PH, relatively small additional CSPs were induced (middle panel). However addition of C 6 -PtdSer (100 μm) to a FAPP1-PH sample whichh had been pre-bound to DPC-CHAPS micelles containing PtdIns(4)P (200 μm) induced substantial additional CSPs (bottom panel). Thus C 6 -PtdSer binding to FAPP1-PH appears to particularly stabilize its PtdIns(4)P micelle complex. The 15 N, 1 H HSQC spectra were collected at 800 MHz in the NMR buffer.
10 FAPP1-PH forms a monomeric state The oligomeric state of the wild type and C94S mutant forms were evaluated by NMR and confirmed by analytical ultracentrifugation in presence of β-mercoptoethanol. Figure S8: The diffusion coefficient (D) of a sample containing 200 μm FAPP1-PH was deduced from NMR diffusion experiments (Nesmelova et al., 2004) at 800 MHz by varying the amplitude of the field gradients. The monomeric state of the protein in solution was deduced from D = x m 2.s -1 which corresponds to a radius of Å for a spherical protein ln I(g 2 )/I(0) -2-3 k 2 (cm 2.s -1 ) Where, ln (A(g 2 )/A(0))=-Dk 2 and k 2 =(γ H ) 2 δ 2 g 2 (Δ-δ/3) The delay and values used for these experiments are described elsewhere (Nesmelova et al., 2004). The field strength g was varied from 5.6 to 53.3 G.cm -1 and the molecular size was deduced from the Stokes-Einstein equation for spherical particles.
11 Figure S9: The purified wild type and C94S mutant proteins yielded similar 1D 1 H NMR spectra. Both proteins were monomeric under reducing conditions based on analytical ultracentrifugation in a Beckman XL-I Protein Characterization System (Beckman Coulter) equipped with an An-50-Ti rotor. Samples were prepared in Tris buffer 20mM ph 7, NaCl 100mM, β-mercapto ethanol 9.6mM and loaded in double sector cells. Velocity sedimentation was performed at 20 C at rotations per minute. The sample was detected at a wavelength of 280nm, and data were processed in SEDFIT (Brown and Schuck, 2006) resulting in frictional ratios for the wild type and C94S mutant of 1.39S and 1.71S, respectively.
12 Table SI. Primers for GST-FAPP2 mutants Y11L12-EE Forward 5 -TGT ACA AGT GGA CCA ACG AAG AGA GCG GTT GGC AGC CTA GAT GG-3 Reverse 5 -CCA TCT AGG CTG CCA ACC GCT CTC TTC GTT GGT CCA CTT GTA CA-3 Y11L12-GG Forward 5 -TAC AAG TGG ACC AAC GGT GGG AGC GGT TGG CAG CCT AGA TGG-3 Reverse 5 -CCA TCT AGG CTG CCA ACC GCT CCC ACC GTT GGT CCA CTT GTA-3
13 Table SII. Statistics for the ensemble of FAPP1-PH domain solution structures Experimental restraints NOE distance restraints 1560 Unambiguous 893 Long range 170 Medium 21 Short 66 Intra residue 428 Sequential 208 Ambiguous 629 HB constraints 38 Talos dihedral constraints 103 Residual experimental violations a NOE > 0.5 Å 0 NOE > 0.3 Å 3 Dihedral restraints > 5 Å 2 Energies (Kcal.mol -1 ) Total ± E noe ± 4.70 E cdih 8.60 ± 1.31 E bond ± 1.47 E improper ± E angle ± 7.85 E vdw ± E dihe ± 5.46 Deviation from idealized geometry Bonds / Angles 0.53 ± 0.02 Impropers 1.33 ± 0.13 Atomic pairwise rmsd (Å) b Backbone atoms 0.26 Heavy atoms 0.80 Ramachandran statistics c Residues in core regions 82.6% Residues in allowed regions 14.4% Residues in generous regions 2.7% Residues in disallowed regions 0.3% a Sum of violations for the ensemble of structures b RMSD is calculated for secondary structural elements including residues 1-7,16-22,26-30,43-44,50-53,61-64,69-73 and c Non glycine residues
14 Table SIII. Structural statistics of the best 20 models of FAPP1-PH/DPC micelles Experimental parameters a Ambiguous distance restraints Number of flexible residues b Atomic pairwise rmsd (Å) All backbone Flexible interface backbone 10 including NH of N10, L12, T13,G14, NHε of W8,W15,Q16 and NH δ of N10 23 (K7 to R18, E50, D57 and G67-A75) Å Å Intermolecular energies (kcal.mol -1 ) E vdw ± E elec ± E restraints 3.73 ± 3.40 Buried surface area ± Distance / insertion angle Micelles center coordinates in Protein inertia frame r (micelle-protein centres) ± 0.85 Å θ (deg) ± 4.01 ψ (deg) ± a deduced from intensity reductions observed in presence of 14-doxyl derivative b according to their surface accessibility and the chemical shift perturbation in presence of DPC/CHAPS
15 Table SIV. Interactions of the Ins(1,4)P 2 head group docked into the FAPP1-PH domain. The sum of VDW radii were used to identify the interacting residues in ADT (scaling factor 1). Amino acid residues involved in intermolecular hydrogen bonds for more than 50% of the docked structures are indicated in bold. Cluster number Population Binding free energy (kcal.mol -1 ) Interacting residues K7,W8,T9,N10,R18,F20,H70,F K7,W8,T9,R18,Y29,H70,F K7,W8,T9,N10,H70,F71
16 References Brown PH and Schuck P. (2006) Macromolecular size-and-shape distributions by sedimentation velocity analytical ultracentrifugation. Biophys J, 90, Dancea F, Kami K and Overduin M. (2008) Lipid interaction networks of peripheral membrane proteins revealed by data-driven micelle docking. Biophys J, 94, Hassinen T and Perakyla M. (2001) New energy terms for reduced protein models implemented in an off-lattice force field. J Comput Chem, 22, Nesmelova IV, Idiyatullin D and Mayo KH. (2004) Measuring protein self-diffusion in protein-protein mixtures using a pulsed gradient spin-echo technique with WATERGATE and isotope filtering. J Magn Reson, 166,
17 Supplementary movies Membrane deformation monitored by DIC FAPP1-PH.avi
Supplementary Table 3. 3 UTR primer sequences. Primer sequences used to amplify and clone the 3 UTR of each indicated gene are listed.
Supplemental Figure 1. DLKI-DIO3 mirna/mrna complementarity. Complementarity between the indicated DLK1-DIO3 cluster mirnas and the UTR of SOX2, SOX9, HIF1A, ZEB1, ZEB2, STAT3 and CDH1with mirsvr and PhastCons
More informationSupplementary Materials
Supplementary Materials 1 Supplementary Table 1. List of primers used for quantitative PCR analysis. Gene name Gene symbol Accession IDs Sequence range Product Primer sequences size (bp) β-actin Actb gi
More informationa) Primary cultures derived from the pancreas of an 11-week-old Pdx1-Cre; K-MADM-p53
1 2 3 4 5 6 7 8 9 10 Supplementary Figure 1. Induction of p53 LOH by MADM. a) Primary cultures derived from the pancreas of an 11-week-old Pdx1-Cre; K-MADM-p53 mouse revealed increased p53 KO/KO (green,
More informationc Tuj1(-) apoptotic live 1 DIV 2 DIV 1 DIV 2 DIV Tuj1(+) Tuj1/GFP/DAPI Tuj1 DAPI GFP
Supplementary Figure 1 Establishment of the gain- and loss-of-function experiments and cell survival assays. a Relative expression of mature mir-484 30 20 10 0 **** **** NCP mir- 484P NCP mir- 484P b Relative
More informationFigure S1. Analysis of genomic and cdna sequences of the targeted regions in WT-KI and
Figure S1. Analysis of genomic and sequences of the targeted regions in and indicated mutant KI cells, with WT and corresponding mutant sequences underlined. (A) cells; (B) K21E-KI cells; (C) D33A-KI cells;
More informationSupplementary Appendix
Supplementary Appendix This appendix has been provided by the authors to give readers additional information about their work. Supplement to: Sherman SI, Wirth LJ, Droz J-P, et al. Motesanib diphosphate
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 U1 inhibition causes a shift of RNA-seq reads from exons to introns. (a) Evidence for the high purity of 4-shU-labeled RNAs used for RNA-seq. HeLa cells transfected with control
More informationSupplemental Data. Shin et al. Plant Cell. (2012) /tpc YFP N
MYC YFP N PIF5 YFP C N-TIC TIC Supplemental Data. Shin et al. Plant Cell. ()..5/tpc..95 Supplemental Figure. TIC interacts with MYC in the nucleus. Bimolecular fluorescence complementation assay using
More informationSupplementary Figure 1. ROS induces rapid Sod1 nuclear localization in a dosagedependent manner. WT yeast cells (SZy1051) were treated with 4NQO at
Supplementary Figure 1. ROS induces rapid Sod1 nuclear localization in a dosagedependent manner. WT yeast cells (SZy1051) were treated with 4NQO at different concentrations for 30 min and analyzed for
More informationTransient β-hairpin Formation in α-synuclein Monomer Revealed by Coarse-grained Molecular Dynamics Simulation
Transient β-hairpin Formation in α-synuclein Monomer Revealed by Coarse-grained Molecular Dynamics Simulation Hang Yu, 1, 2, a) Wei Han, 1, 3, b) Wen Ma, 1, 2 1, 2, 3, c) and Klaus Schulten 1) Beckman
More informationSupplementary Document
Supplementary Document 1. Supplementary Table legends 2. Supplementary Figure legends 3. Supplementary Tables 4. Supplementary Figures 5. Supplementary References 1. Supplementary Table legends Suppl.
More informationAbbreviations: P- paraffin-embedded section; C, cryosection; Bio-SA, biotin-streptavidin-conjugated fluorescein amplification.
Supplementary Table 1. Sequence of primers for real time PCR. Gene Forward primer Reverse primer S25 5 -GTG GTC CAC ACT ACT CTC TGA GTT TC-3 5 - GAC TTT CCG GCA TCC TTC TTC-3 Mafa cds 5 -CTT CAG CAA GGA
More informationCD31 5'-AGA GAC GGT CTT GTC GCA GT-3' 5 ' -TAC TGG GCT TCG AGA GCA GT-3'
Table S1. The primer sets used for real-time RT-PCR analysis. Gene Forward Reverse VEGF PDGFB TGF-β MCP-1 5'-GTT GCA GCA TGA ATC TGA GG-3' 5'-GGA GAC TCT TCG AGG AGC ACT T-3' 5'-GAA TCA GGC ATC GAG AGA
More informationSupplementary Figure 1 a
Supplementary Figure a Normalized expression/tbp (A.U.).6... Trip-br transcripts Trans Trans Trans b..5. Trip-br Ctrl LPS Normalized expression/tbp (A.U.) c Trip-br transcripts. adipocytes.... Trans Trans
More informationSupplementary Figures
Supplementary Figures Supplementary Figure 1. H3F3B expression in lung cancer. a. Comparison of H3F3B expression in relapsed and non-relapsed lung cancer patients. b. Prognosis of two groups of lung cancer
More informationSUPPORTING INFORMATION
SUPPORTING INFORMATION Biology is different in small volumes: endogenous signals shape phenotype of primary hepatocytes cultured in microfluidic channels Amranul Haque, Pantea Gheibi, Yandong Gao, Elena
More informationSupplementary Figure 1 MicroRNA expression in human synovial fibroblasts from different locations. MicroRNA, which were identified by RNAseq as most
Supplementary Figure 1 MicroRNA expression in human synovial fibroblasts from different locations. MicroRNA, which were identified by RNAseq as most differentially expressed between human synovial fibroblasts
More informationResistance to Tetracycline Antibiotics by Wangrong Yang, Ian F. Moore, Kalinka P. Koteva, Donald W. Hughes, David C. Bareich and Gerard D. Wright.
Supplementary Data for TetX is a Flavin-Dependent Monooxygenase Conferring Resistance to Tetracycline Antibiotics by Wangrong Yang, Ian F. Moore, Kalinka P. Koteva, Donald W. Hughes, David C. Bareich and
More informationA smart acid nanosystem for ultrasensitive. live cell mrna imaging by the target-triggered intracellular self-assembly
Electronic Supplementary Material (ESI) for Chemical Science. This journal is The Royal Society of Chemistry 2017 A smart ZnO@polydopamine-nucleic acid nanosystem for ultrasensitive live cell mrna imaging
More informationCitation for published version (APA): Oosterveer, M. H. (2009). Control of metabolic flux by nutrient sensors Groningen: s.n.
University of Groningen Control of metabolic flux by nutrient sensors Oosterveer, Maaike IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it.
More informationSupporting Information
Supporting Information Chen et al. 10.1073/pnas.1106420108 SI Materials and Methods High-Level Expression of Human apoe3. A monomeric, biologically active, full-length human apoe3 is generated using an
More informationList of Figures. List of Tables
Supporting Information for: Signaling Domain of Sonic Hedgehog as Cannibalistic Calcium-Regulated Zinc-Peptidase Rocio Rebollido-Rios 1, Shyam Bandari 3, Christoph Wilms 1, Stanislav Jakuschev 1, Andrea
More informationSupplementary Materials for
advances.sciencemag.org/cgi/content/full/4/3/eaaq0762/dc1 Supplementary Materials for Structures of monomeric and oligomeric forms of the Toxoplasma gondii perforin-like protein 1 Tao Ni, Sophie I. Williams,
More informationToluidin-Staining of mast cells Ear tissue was fixed with Carnoy (60% ethanol, 30% chloroform, 10% acetic acid) overnight at 4 C, afterwards
Toluidin-Staining of mast cells Ear tissue was fixed with Carnoy (60% ethanol, 30% chloroform, 10% acetic acid) overnight at 4 C, afterwards incubated in 100 % ethanol overnight at 4 C and embedded in
More informationNature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Design of isolated protein and RNC constructs, and homogeneity of purified RNCs. (a) Schematic depicting the design and nomenclature used for all the isolated proteins and RNCs used
More informationSUPPLEMENTARY INFORMATION
doi: 10.1038/nature05883 SUPPLEMENTARY INFORMATION Supplemental Figure 1 Prostaglandin agonists and antagonists alter runx1/cmyb expression. a-e, Embryos were exposed to (b) PGE2 and (c) PGI2 (20μM) and
More informationChapter VI. Increased affinity in the complex of yeast cytochrome c and cytochrome c peroxidase
Chapter VI Increased affinity in the complex of yeast cytochrome c and cytochrome c peroxidase Chapter VI Abstract We report the study of T12A Cyt c CcP complex using isothermal titration calorimetry (ITC),
More informationSUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature10743 Supplementary Figures and Legends Supplementary Figure 1. CYP17A1 (red boxes) lies at the intersection of steroid hormone biosynthetic pathways. CYP17A1
More informationPlasmids Western blot analysis and immunostaining Flow Cytometry Cell surface biotinylation RNA isolation and cdna synthesis
Plasmids psuper-retro-s100a10 shrna1 was constructed by cloning the dsdna oligo 5 -GAT CCC CGT GGG CTT CCA GAG CTT CTT TCA AGA GAA GAA GCT CTG GAA GCC CAC TTT TTA-3 and 5 -AGC TTA AAA AGT GGG CTT CCA GAG
More informationSupplementary Material
Supplementary Material Materials and methods Enzyme assay The enzymatic activity of -glucosidase toward salicin was measured with the Miller method (Miller, 1959) using glucose as the standard. A total
More informationSupplementary Table 2. Conserved regulatory elements in the promoters of CD36.
Supplementary Table 1. RT-qPCR primers for CD3, PPARg and CEBP. Assay Forward Primer Reverse Primer 1A CAT TTG TGG CCT TGT GCT CTT TGA TGA GTC ACA GAA AGA ATC AAT TC 1B AGG AAA TGA ACT GAT GAG TCA CAG
More informationCS612 - Algorithms in Bioinformatics
Spring 2016 Protein Structure February 7, 2016 Introduction to Protein Structure A protein is a linear chain of organic molecular building blocks called amino acids. Introduction to Protein Structure Amine
More informationJournal of Cell Science Supplementary information. Arl8b +/- Arl8b -/- Inset B. electron density. genotype
J. Cell Sci. : doi:.4/jcs.59: Supplementary information E9. A Arl8b /- Arl8b -/- Arl8b Arl8b non-specific band Gapdh Tbp E7.5 HE Inset B D Control al am hf C E Arl8b -/- al am hf E8.5 F low middle high
More informationDescription of Supplementary Files. File Name: Supplementary Information Description: Supplementary Figures and Supplementary Tables
Description of Supplementary Files File Name: Supplementary Information Description: Supplementary Figures and Supplementary Tables Supplementary Figure 1: (A), HCT116 IDH1-WT and IDH1-R132H cells were
More informationPhylogenetic analysis of human and chicken importins. Only five of six importins were studied because
Supplementary Figure S1 Phylogenetic analysis of human and chicken importins. Only five of six importins were studied because importin-α6 was shown to be testis-specific. Human and chicken importin protein
More informationCulture Density (OD600) 0.1. Culture Density (OD600) Culture Density (OD600) Culture Density (OD600) Culture Density (OD600)
A. B. C. D. E. PA JSRI JSRI 2 PA DSAM DSAM 2 DSAM 3 PA LNAP LNAP 2 LNAP 3 PAO Fcor Fcor 2 Fcor 3 PAO Wtho Wtho 2 Wtho 3 Wtho 4 DTSB Low Iron 2 4 6 8 2 4 6 8 2 22 DTSB Low Iron 2 4 6 8 2 4 6 8 2 22 DTSB
More informationSUPPLEMENTARY DATA. Supplementary Table 1. Primer sequences for qrt-pcr
Supplementary Table 1. Primer sequences for qrt-pcr Gene PRDM16 UCP1 PGC1α Dio2 Elovl3 Cidea Cox8b PPARγ AP2 mttfam CyCs Nampt NRF1 16s-rRNA Hexokinase 2, intron 9 β-actin Primer Sequences 5'-CCA CCA GCG
More informationIntegration Solutions
Integration Solutions (1) a) With no active glycosyltransferase of either type, an ii individual would not be able to add any sugars to the O form of the lipopolysaccharide. Thus, the only lipopolysaccharide
More informationNature Immunology: doi: /ni.3836
Supplementary Figure 1 Recombinant LIGHT-VTP induces pericyte contractility and endothelial cell activation. (a) Western blot showing purification steps for full length murine LIGHT-VTP (CGKRK) protein:
More informationBeta Thalassemia Case Study Introduction to Bioinformatics
Beta Thalassemia Case Study Sami Khuri Department of Computer Science San José State University San José, California, USA sami.khuri@sjsu.edu www.cs.sjsu.edu/faculty/khuri Outline v Hemoglobin v Alpha
More informationTable S1. Oligonucleotides used for the in-house RT-PCR assays targeting the M, H7 or N9. Assay (s) Target Name Sequence (5 3 ) Comments
SUPPLEMENTAL INFORMATION 2 3 Table S. Oligonucleotides used for the in-house RT-PCR assays targeting the M, H7 or N9 genes. Assay (s) Target Name Sequence (5 3 ) Comments CDC M InfA Forward (NS), CDC M
More informationSDS-Assisted Protein Transport Through Solid-State Nanopores
Supplementary Information for: SDS-Assisted Protein Transport Through Solid-State Nanopores Laura Restrepo-Pérez 1, Shalini John 2, Aleksei Aksimentiev 2 *, Chirlmin Joo 1 *, Cees Dekker 1 * 1 Department
More informationSupplementary Materials. High affinity binding of phosphatidylinositol-4-phosphate. by Legionella pneumophila DrrA
Supplementary Materials High affinity binding of phosphatidylinositol-4-phosphate by Legionella pneumophila DrrA Running title: Molecular basis of PtdIns(4)P-binding by DrrA Stefan Schoebel, Wulf Blankenfeldt,
More informationSupplementary Figure 1
Metastatic melanoma Primary melanoma Healthy human skin Supplementary Figure 1 CD22 IgG4 Supplementary Figure 1: Immunohisochemical analysis of CD22+ (left) and IgG4 (right), cells (shown in red and indicated
More informationUnveiling transient protein-protein interactions that modulate inhibition of alpha-synuclein aggregation
Supplementary information Unveiling transient protein-protein interactions that modulate inhibition of alpha-synuclein aggregation by beta-synuclein, a pre-synaptic protein that co-localizes with alpha-synuclein.
More informationChapter 3. Structure of Enzymes. Enzyme Engineering
Chapter 3. Structure of Enzymes Enzyme Engineering 3.1 Introduction With purified protein, Determining M r of the protein Determining composition of amino acids and the primary structure Determining the
More informationAstaxanthin prevents and reverses diet-induced insulin resistance and. steatohepatitis in mice: A comparison with vitamin E
Supplementary Information Astaxanthin prevents and reverses diet-induced insulin resistance and steatohepatitis in mice: A comparison with vitamin E Yinhua Ni, 1,2 Mayumi Nagashimada, 1 Fen Zhuge, 1 Lili
More informationSupplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random
S1 Supplementary Figure 1 (previous page). EM analysis of full-length GCGR. (a) Exemplary tilt pair images of the GCGR mab23 complex acquired for Random Conical Tilt (RCT) reconstruction (left: -50,right:
More informationwww.lessonplansinc.com Topic: Protein Synthesis - Sentence Activity Summary: Students will simulate transcription and translation by building a sentence/polypeptide from words/amino acids. Goals & Objectives:
More informationSupplementary Figure 1
Supplementary Figure 1 Supplementary Figure 1. Lats1/2 deleted ihbs and ihps showed decreased transcripts of hepatocyte related genes (a and b) Western blots (a) and recombination PCR (b) of control and
More informationMechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis SUPPLEMENTARY INFORMATION
Mechanistic and functional insights into fatty acid activation in Mycobacterium tuberculosis Pooja Arora 1, Aneesh Goyal 2, Vivek T atarajan 1, Eerappa Rajakumara 2, Priyanka Verma 1, Radhika Gupta 3,
More informationSingle-Molecule Analysis of Gene Expression Using Two-Color RNA- Labeling in Live Yeast
Supplemental Figures, Tables and Results Single-Molecule Analysis of Gene Expression Using Two-Color RNA- Labeling in Live Yeast Sami Hocine 1, Pascal Raymond 2, Daniel Zenklusen 2, Jeffrey A. Chao 1 &
More informationSupplementary Figure 1a
Supplementary Figure 1a Hours: E-cadherin TGF-β On TGF-β Off 0 12 24 36 48 24 48 72 Vimentin βactin Fig. S1a. Treatment of AML12 cells with TGF-β induces EMT. Treatment of AML12 cells with TGF-β results
More informationPatterns of hemagglutinin evolution and the epidemiology of influenza
2 8 US Annual Mortality Rate All causes Infectious Disease Patterns of hemagglutinin evolution and the epidemiology of influenza DIMACS Working Group on Genetics and Evolution of Pathogens, 25 Nov 3 Deaths
More information(B D) Three views of the final refined 2Fo-Fc electron density map of the Vpr (red)-ung2 (green) interacting region, contoured at 1.4σ.
Supplementary Figure 1 Overall structure of the DDB1 DCAF1 Vpr UNG2 complex. (A) The final refined 2Fo-Fc electron density map, contoured at 1.4σ of Vpr, illustrating well-defined side chains. (B D) Three
More informationSupplementary Figure 1. Structure models of the c4 variant proteins based on the structures of maltose binding protein (MBP) in red and TEM-1
Supplementary Figure 1. Structure models of the c4 variant proteins based on the structures of maltose binding protein (MBP) in red and TEM-1 β-lactamase (BLA) in blue. (a) c4 model and the close-up view
More informationEngineering a polarity-sensitive biosensor for time-lapse imaging of apoptotic processes and degeneration
nature methods Engineering a polarity-sensitive biosensor for time-lapse imaging of apoptotic processes and degeneration Yujin E Kim, Jeannie Chen, Jonah R Chan & Ralf Langen Supplementary figures and
More informationA basic helix loop helix transcription factor controls cell growth
A basic helix loop helix transcription factor controls cell growth and size in root hairs Keke Yi 1,2, Benoît Menand 1,3, Elizabeth Bell 1, Liam Dolan 1,4 Supplementary note Low soil phosphate availability
More informationThis exam consists of two parts. Part I is multiple choice. Each of these 25 questions is worth 2 points.
MBB 407/511 Molecular Biology and Biochemistry First Examination - October 1, 2002 Name Social Security Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions is
More informationSupplementary Information A Hydrophobic Barrier Deep Within the Inner Pore of the TWIK-1 K2P Potassium Channel Aryal et al.
Supplementary Information A Hydrophobic Barrier Deep Within the Inner Pore of the TWIK-1 K2P Potassium Channel Aryal et al. Supplementary Figure 1 TWIK-1 stability during MD simulations in a phospholipid
More informationCoarse grained simulations of Lipid Bilayer Membranes
Coarse grained simulations of Lipid Bilayer Membranes P. B. Sunil Kumar Department of Physics IIT Madras, Chennai 600036 sunil@iitm.ac.in Atomistic MD: time scales ~ 10 ns length scales ~100 nm 2 To study
More informationLezione 10. Sommario. Bioinformatica. Lezione 10: Sintesi proteica Synthesis of proteins Central dogma: DNA makes RNA makes proteins Genetic code
Lezione 10 Bioinformatica Mauro Ceccanti e Alberto Paoluzzi Lezione 10: Sintesi proteica Synthesis of proteins Dip. Informatica e Automazione Università Roma Tre Dip. Medicina Clinica Università La Sapienza
More informationSupplementary Materials for
www.sciencesignaling.org/cgi/content/full/10/473/eaai7696/dc1 Supplementary Materials for Astrocyte-shed extracellular vesicles regulate the peripheral leukocyte response to inflammatory brain lesions
More informationBHP 2-7 and Nthy-ori 3-1 cells were grown in RPMI1640 medium (Hyclone) supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine, and 100 U/mL
1 2 3 4 Materials and Methods Cell culture BHP 2-7 and Nthy-ori 3-1 cells were grown in RPMI1640 medium (Hyclone) 5 supplemented with 10% fetal bovine serum (Gibco), 2mM L-glutamine, and 100 U/mL 6 penicillin-streptomycin.
More informationTable S1. X-ray data collection and refinement statistics
Table S1. X-ray data collection and refinement statistics Data collection H7.167 Fab-Sh2/H7 complex Beamline SSRL 12-2 Wavelength (Å) 0.97950 Space group I2 1 3 Unit cell parameters (Å, º) a = b = c=207.3,
More informationBeta Thalassemia Sami Khuri Department of Computer Science San José State University Spring 2015
Bioinformatics in Medical Product Development SMPD 287 Three Beta Thalassemia Sami Khuri Department of Computer Science San José State University Hemoglobin Outline Anatomy of a gene Hemoglobinopathies
More informationSupplementary Information
Supplementary Information Remodeling of heterochromatin structure slows neuropathological progression and prolongs survival in an animal model of Huntington s disease Junghee Lee, Yu Jin Hwang, Yunha Kim,
More informationRelationship of the APOA5/A4/C3/A1 gene cluster and APOB gene polymorphisms with dyslipidemia
elationship of the APOA5/A4/C3/A1 gene cluster and APOB gene polymorphisms with dyslipidemia H.J. Ou 1, G. Huang 2, W. Liu 3, X.L. Ma 2, Y. Wei 4, T. Zhou 5 and Z.M. Pan 3 1 Department of Neurology, The
More informationCross-talk between mineralocorticoid and angiotensin II signaling for cardiac
ONLINE SUPPLEMENT TO Crosstalk between mineralocorticoid and angiotensin II signaling for cardiac remodeling An Di ZHANG,,3, Aurelie NGUYEN DINH CAT*,,3, Christelle SOUKASEUM *,,3, Brigitte ESCOUBET, 4,
More informationSupplementary Figure 1
Supplementary Figure 1 3 3 3 1 1 Bregma -1.6mm 3 : Bregma Ref) Http://www.mbl.org/atlas165/atlas165_start.html Bregma -.18mm Supplementary Figure 1 Schematic representation of the utilized brain slice
More informationLecture 15. Membrane Proteins I
Lecture 15 Membrane Proteins I Introduction What are membrane proteins and where do they exist? Proteins consist of three main classes which are classified as globular, fibrous and membrane proteins. A
More informationLecture 10 More about proteins
Lecture 10 More about proteins Today we're going to extend our discussion of protein structure. This may seem far-removed from gene cloning, but it is the path to understanding the genes that we are cloning.
More informationSupplementary Table 1. Data collection and refinement statistics (molecular replacement).
Supplementary Table 1. Data collection and refinement statistics (molecular replacement). Data set statistics HLA A*0201- ALWGPDPAAA PPI TCR PPI TCR/A2- ALWGPDPAAA PPI TCR/A2- ALWGPDPAAA Space Group P2
More informationSupporting Information
Supporting Information Guan et al. 10.1073/pnas.1217609110 Fig. S1. Three patterns of reactivity for CD4-induced (CD4i) mabs. The following representative ELISAs show three patterns of reactivity for CD4i
More informationSupplementary Figure 1: Loop conversion from inactive (0 ns) to pre-active (75 ns) observed in MD2. The plot monitors the RMSD calculated for
Supplementary Figure 1: Loop conversion from inactive (0 ns) to pre-active (75 ns) observed in MD2. The plot monitors the RMSD calculated for residues 3 to 345 and backbone atoms of the 344-loop using
More informationSupporting material. Membrane permeation induced by aggregates of human islet amyloid polypeptides
Supporting material Membrane permeation induced by aggregates of human islet amyloid polypeptides Chetan Poojari Forschungszentrum Jülich GmbH, Institute of Complex Systems: Structural Biochemistry (ICS-6),
More informationSupporting Information
Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 018 Supporting Information Modulating Interactions between Ligand-Coated Nanoparticles and Phase-Separated
More informationSupplementary Information. Bamboo shoot fiber prevents obesity in mice by. modulating the gut microbiota
Supplementary Information Bamboo shoot fiber prevents obesity in mice by modulating the gut microbiota Xiufen Li 1,2, Juan Guo 1, Kailong Ji 1,2, and Ping Zhang 1,* 1 Key Laboratory of Tropical Plant Resources
More informationSupplementary Figures
Supplementary Figures Supplementary Figure 1. (a) Uncropped version of Fig. 2a. RM indicates that the translation was done in the absence of rough mcirosomes. (b) LepB construct containing the GGPG-L6RL6-
More informationSimulationen von Lipidmembranen
Simulationen von Lipidmembranen Thomas Stockner Thomas.stockner@meduniwien.ac.at Summary Methods Force Field MD simulations Membrane simulations Application Oxidized lipids Anesthetics Molecular biology
More informationBaseline clinical characteristics for the 81 CMML patients Routine diagnostic testing and statistical analyses... 3
Next-Generation Sequencing Technology Reveals a Characteristic Pattern of Molecular Mutations in 72.8% of Chronic Myelomonocytic Leukemia (CMML) by Detecting Frequent Alterations in TET2, CBL, RAS, and
More informationAdvanced Subsidiary Unit 1: Lifestyle, Transport, Genes and Health
Write your name here Surname Other names Edexcel GCE Centre Number Candidate Number Biology Advanced Subsidiary Unit 1: Lifestyle, Transport, Genes and Health Thursday 8 January 2009 Morning Time: 1 hour
More informationSupplementary Information: Liquid-liquid phase coexistence in lipid membranes observed by natural abundance 1 H 13 C solid-state NMR
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the wner Societies 28 Supplementary Information: Liquid-liquid phase coexistence in lipid membranes observed
More informationBilayer Deformation, Pores & Micellation Induced by Oxidized Lipids
Supporting Information Bilayer Deformation, Pores & Micellation Induced by Oxidized Lipids Phansiri Boonnoy 1, Viwan Jarerattanachat 1,2, Mikko Karttunen 3*, and Jirasak Wongekkabut 1* 1 Department of
More informationNucleotide Sequence of the Australian Bluetongue Virus Serotype 1 RNA Segment 10
J. gen. Virol. (1988), 69, 945-949. Printed in Great Britain 945 Key words: BTV/genome segment lo/nucleotide sequence Nucleotide Sequence of the Australian Bluetongue Virus Serotype 1 RNA Segment 10 By
More informationMBB 694:407, 115:511. Please use BLOCK CAPITAL letters like this --- A, B, C, D, E. Not lowercase!
MBB 694:407, 115:511 First Test Severinov/Deis Tue. Sep. 30, 2003 Name Index number (not SSN) Row Letter Seat Number This exam consists of two parts. Part I is multiple choice. Each of these 25 questions
More informationTetR repressor-based bioreporters for the detection of doxycycline using Escherichia
Supplementary materials TetR repressor-based bioreporters for the detection of doxycycline using Escherichia coli and Acinetobacter oleivorans Hyerim Hong and Woojun Park * Department of Environmental
More informationProtein Secondary Structure
Protein Secondary Structure Reading: Berg, Tymoczko & Stryer, 6th ed., Chapter 2, pp. 37-45 Problems in textbook: chapter 2, pp. 63-64, #1,5,9 Directory of Jmol structures of proteins: http://www.biochem.arizona.edu/classes/bioc462/462a/jmol/routines/routines.html
More informationSupplementary Table 1. Properties of lysates of E. coli strains expressing CcLpxI point mutants
Supplementary Table 1. Properties of lysates of E. coli strains expressing CcLpxI point mutants Species UDP-2,3- diacylglucosamine hydrolase specific activity (nmol min -1 mg -1 ) Fold vectorcontrol specific
More informationSupporting Information. Mutational analysis of a phenazine biosynthetic gene cluster in
Supporting Information for Mutational analysis of a phenazine biosynthetic gene cluster in Streptomyces anulatus 9663 Orwah Saleh 1, Katrin Flinspach 1, Lucia Westrich 1, Andreas Kulik 2, Bertolt Gust
More informationBiosci., Vol. 5, Number 4, December 1983, pp
Biosci., Vol. 5, Number 4, December 1983, pp. 311-320. Printed in India. Denaturation of the high molecular weight protein fraction of mustard (Brassica juncea) and rapeseed (Brassica campestris) by urea
More informationChemical Surface Transformation 1
Chemical Surface Transformation 1 Chemical reactions at Si H surfaces (inorganic and organic) can generate very thin films (sub nm thickness up to µm): inorganic layer formation by: thermal conversion:
More informationTable S1: Kinetic parameters of drug and substrate binding to wild type and HIV-1 protease variants. Data adapted from Ref. 6 in main text.
Dynamical Network of HIV-1 Protease Mutants Reveals the Mechanism of Drug Resistance and Unhindered Activity Rajeswari Appadurai and Sanjib Senapati* BJM School of Biosciences and Department of Biotechnology,
More informationWe parameterized a coarse-grained fullerene consistent with the MARTINI coarse-grained force field
Parameterization of the fullerene coarse-grained model We parameterized a coarse-grained fullerene consistent with the MARTINI coarse-grained force field for lipids 1 and proteins 2. In the MARTINI force
More informationDetergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site.
Supplementary Figure 1 Detergent solubilised 5 TMD binds pregnanolone at the Q245 neurosteroid potentiation site. (a) Gel filtration profiles of purified 5 TMD samples at 100 nm, heated beforehand for
More informationSecondary Structure North 72nd Street, Wauwatosa, WI Phone: (414) Fax: (414) dmoleculardesigns.com
Secondary Structure In the previous protein folding activity, you created a generic or hypothetical 15-amino acid protein and learned that basic principles of chemistry determine how each protein spontaneously
More informationCIRCRESAHA/2004/098145/R1 - ONLINE 1. Validation by Semi-quantitative Real-Time Reverse Transcription PCR
CIRCRESAHA/2004/098145/R1 - ONLINE 1 Expanded Materials and Methods Validation by Semi-quantitative Real-Time Reverse Transcription PCR Expression patterns of 13 genes (Online Table 2), selected with respect
More informationSupplemental Information. Cancer-Associated Fibroblasts Neutralize. the Anti-tumor Effect of CSF1 Receptor Blockade
Cancer Cell, Volume 32 Supplemental Information Cancer-Associated Fibroblasts Neutralize the Anti-tumor Effect of CSF1 Receptor Blockade by Inducing PMN-MDSC Infiltration of Tumors Vinit Kumar, Laxminarasimha
More informationFluid Mozaic Model of Membranes
Replacement for the 1935 Davson Danielli model Provided explanation for Gortner-Grendel lack of lipid and permitted the unit membrane model. Trans membrane protein by labelling Fry & Edidin showed that
More informationSupplemental Information. Th17 Lymphocytes Induce Neuronal. Cell Death in a Human ipsc-based. Model of Parkinson's Disease
Cell Stem Cell, Volume 23 Supplemental Information Th17 Lymphocytes Induce Neuronal Cell Death in a Human ipsc-based Model of Parkinson's Disease Annika Sommer, Franz Maxreiter, Florian Krach, Tanja Fadler,
More information