Rho1 binding site PtdIns(4,5)P2 binding site Both sites
|
|
|
- Ashlie Clarke
- 5 years ago
- Views:
Transcription
1 localization Mutation site DMSO LatB WT F77A I115A I131A K134A Rho1 binding site PtdIns(4,5)P2 binding site Both sites E186A E199A N201A R84A-E186A-E199A L131A-K136A-E186A L131A-E186A-E199A K136A-E186A-E199A K136A-E186A-N201A L131A-K136A-E186A-E199A K155A-R157A K135A-K155A-R157A R137A-K155A-R157A K135A-R137A-K155A-R157A R137A-K155A-K194A-Y196A K155A-R157A-K194A-Y196A R137A-K155A-R157A-K194A-Y196A R137A-K155A-R157A-R168A-K194A K135A-R137A-K155A-R157A-R168A-K194A L131A-K136A-E199A-K135A-R137A- K155A-R157A-R168A-K194A-Y196A Depolarized N Depolarized Supplementary Table 1 In vivo localization of yeast Sec3 mutants
2 Vesicle Vesicle GTP Ral Rab11 GTP GTP Sec4 Exo84 Sec5 Sec15 Sec10 Sec6 Sec8 GTP TC10 Exo70 Sec3 PI(4,5)P 2 The exocyst complex GTP Rho3 Sec15 Sec10 Exo84 Sec6 Sec5 Sec8 Exo70 Sec3 PI(4,5)P 2 PI(4,5)P 2 Rho1 GTP Cdc42 The exocyst complex Plasma membrane Plasma membrane Mammalian Yeast Supplementary Figure 1 Schematic drawing of the tethering between the vesicle and the plasma membrane by the exocyst complex
3 PLCβ2 Rac1 Sec3 Rho1 (Rac1) PLCγ2 Rac2 Sec3 Tyr71 Tyr64 Tyr71 Tyr64 Lys136 Arg22 Val43 Val36 Leu74 Leu67 Phe44 Phe37 Pro35 Leu77 Leu70 Leu131 Val43 Val36 Lys136 Leu74 Leu67 Lys67 Phe44 Phe37 Phe102 Leu77 Leu70 Leu131 Trp63 Trp56 PLCβ2 Rho1 (Rac2) Trp63 Trp56 PLCγ2 Supplementary Figure 2 Comparison of the Sec3-N Rho1 interaction with the PLCβ2 Rac2 and PLCγ2 Rac1 interactions The small GTPases are colored pink. The Sec3-N, PLCβ2 (PDB: 2FJU) and PLCγ2 (PDB: 2W2X) are colored in cyan, yellow and orange, respectively. The amino acid residues that are involved in the interactions are represented as sticks. Nature Structural & Molecular Biology: doi: /nsmb.1722
4 Supplementary Figure 3 Protein-lipid overlay assays using Sec3-N mutants GST-fused Sec3-N wild type and mutants were overlaid to various phospholipids spotted to nitrocellulose membranes, and then, the bound proteins were detected by anti-gst antibody. Sec3 mutants we generated in this study abrogate phosphoinositide-binding in vitro.
5 Amino-acid sequence alignment of Sec3-N from fungi α1 Sc Cs An Nc β NSSQTSNFLAEQYERDRKAIINCCFSRPDHKTGEPPNNYITHVRIIEDSKFPSSRPPPDSKLENKKKRLL ASSVNSNFLAEQYDRDRTAIINSCFQKVDPATGTPLNSYITHVRIIEDSRFPSSRPAINSPLENKKKRVL GPGDASMSRAEKFEDEKRRIIHSCFGKKDSDG.SLVESYITHVRILEDAAYPSTPAPPNS.PPENKKPRV RDEDGSSRHATRRSNNKNKTTEG...IDNDE.LAIETYITHIRITEFSTHPTSPPPPQARTPNTEKPRI β2 Sc Cs An Nc β β5 β ILSAKPNNAKLIQIHKARENSDGSFQIGRTWQLTELVRVE...KDLEISEGFILTMSK IVSSQ.SNGKGMQFHKARENSNGTFQIGRTWDLFELELIE...RDVEIPQGFILVMGK IIVAVRRSGR.VRMHKARENNDGSFSIGKTWMLDDLSCIQSYNALVPSTPLEQQHKQWAANVGFIVTVGK IIVAVRKSGR.VRLHKSKENPNGTFSIGKTWFLDDLSDIESFTSPTASP...NFREWAGDVGFIVTLGK α2 β7 Sc Cs An Nc β4 β3 200 β α KYYWETNSAKERTVFIKSLITLYIQTFEGHVPELVNWDLSLFYLDERSYQRAVITNRPGSVS.PIK... KYYWQTNSAKERTVFIKSLVSIFMENTGGRVPKLVNWDLSMFYLDETSYQRAVISKPSGSVS.PVKQRNV PYYWHARTSKEKDFFIGSLVKIYRKYTGGKVPTLIGFDDRER.QLLAGGSAAGPPAPKGPPP.SGPPRPE PYYWQAQTDKEKKFFIASLIKIFGKYTGGRVPRLIGFDQRELDQVLGGAQAPRRPADRGPPSRSGTQIDQ Amino-acid sequence alignment of Sec3-N from vertebrates α1 human mouse zebrafish Xenopus 1 β β4 β MTAIKHALQRDIFTPNDERLLSIVNVCKAGKKKKNCFLCATVTTERPVQVKVVKVKKSDKGDFYKRQIAW MTAIKHALQRDIFTPNDERLLSIVNVCKAGKKKKNCFLCATVTTERPVQVKVVKVKKSDKGDFYKRQIAW MTAIKHALQRDIFTPNDERLLSIVNVCKAGKKKKNCFLCATVTTERPVQVKVVKVKKSDKGDFYKRQMAW MTAIKHALQRDIFTPNDERLLSIVNVCKAGKKKKNCFLCATVTTERPVHVKVVKVKKSDKGDFYKTQTVW β5 human mouse zebrafish Xenopus β3 β3 β β6 90 β7 100 α2 110 β8 120 α3 130 ALRDLAVVDAKDAIKENPEFDLHFEKIYKWVASSTAEKNAFISCIWKLNQRYLRKKIDFVNVSSQL... ALRDLAVVDAKDAIKENPEFDLHFEKVYKWVASSTAEKNAFISCIWKLNQRYLRKKIDFVNVSSQLLEES ELRDLTEVDAKDANKENPEFDLHFEKVYRWVASSTAEKNSFISCIWKLNQRYLRKKVEFVNVSPQLLEES LLRDLAVVDAKDAVKENPDFDLHFDKVYKWVASSIAEKNAFISCLWKLNQRYLRKKIDFANVSSQLLEES Supplementary Figure 4 Amino-acid sequence alignment of the N-terminal region of fungi and vertebrate Sec3 (a) Amino-acid sequence alignment of the N-terminal region of Sec3 from fungi. Identical residues are highlighted by red backgrounds. Similar residues are colored red. The secondary structure of yeast Sec3-N is represented above the alignment. Residues for the potential PtdIns(4,5)P2-binding site are indicated by magenta dots. Sc, Cs, An, and Nc represent Saccharomyces cerevisiae, Candida sphaerica, Aspergillus nidulans, and Neurospora crassa, respectively. (b) Amino-acid sequence alignment of the N-terminal region of Sec3 from vertebrates. Drawing schemes are the same as in a. The predicted secondary structure of the N-terminal region of human Sec3 is represented above the alignment. Nature Structural & Molecular Biology: doi: /nsmb.1722
6 yeastsec3...snflaeqyerd R K A I INCC F SRP D H K TGEPPNNY I TH V R I IEDSKFPSSRPPPDSKLEN KKKR......MTAI K H A L QRDI F TPN D E R...L L SI V N V CKAG... KKKK... MNSLRAVLTCSTMSA K S A I SKEI F APL D E R...M L GA V Q V KRRT... KKKIPFL yeastsec L L I LSA KPNNAKL I Q I H K AR ENSDGSFQIGRT. W Q L TE L VR V EKD..LEI S EG F I L TMSK...NCF L C ATV TTERPVQ V K V V K VK KSDKGDFYKRQIA W A L RD L AV V DAKDAIKE N PE F D L HFEK ATGGQGEYLTY I C LSV TNKKPTQ A S I T K VK QFEGSTSFVRRSQ W M L EQ L RQ V NGIDPNGD S AE F D L LFEN yeastsec K Y.Y W ET NS AK E R TV F IKS L ITLYIQTFEG H VP E L V N WDLS L FY...LDER I Y.K W VA SS TA E K NA F ISC I WKLNQRYLR. K KI D F V N VSSQ L... A F DQ W VA ST AS E K CT F FQI L HHTCQRYLTD R KP E F I N CQSK I MGGNSILHSAADSVTSAVQKASQALNER yeastsec SYQRAVITN.RPGSVSPIKS... GERLGRAEEKTEDLKNSAQQFAETAHKLAM..KHKC Supplementary Figure 5 Amino-acid sequence alignment of yeast Sec3-N, the N-terminal region of human Sec3, and human amysin Drawing schemes are the same as in Supplementary Figure 4.
FW 1 CDR 1 FW 2 CDR 2
Supplementary Figure 1 Supplementary Figure 1: Interface of the E9:Fas structure. The two interfaces formed by V H and V L of E9 with Fas are shown in stereo. The Fas receptor is represented as a surface
Structure and RNA-binding properties. of the Not1 Not2 Not5 module of the yeast Ccr4 Not complex
Structure and RNA-binding properties of the Not1 Not2 Not5 module of the yeast Ccr4 Not complex Varun Bhaskar 1, Vladimir Roudko 2,3, Jerome Basquin 1, Kundan Sharma 4, Henning Urlaub 4, Bertrand Seraphin
Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase Cwc27
Acta Cryst. (2014). D70, doi:10.1107/s1399004714021695 Supporting information Volume 70 (2014) Supporting information for article: Structure and evolution of the spliceosomal peptidyl-prolyl cistrans isomerase
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11524 Supplementary discussion Functional analysis of the sugar porter family (SP) signature motifs. As seen in Fig. 5c, single point mutation of the conserved
Supplementary Information Intrinsic Localized Modes in Proteins
Supplementary Information Intrinsic Localized Modes in Proteins Adrien Nicolaï 1,, Patrice Delarue and Patrick Senet, 1 Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute,
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11085 Supplementary Tables: Supplementary Table 1. Summary of crystallographic and structure refinement data Structure BRIL-NOP receptor Data collection Number of crystals 23 Space group
Supplementary figure 1. Comparison of unbound ogm-csf and ogm-csf as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine
Supplementary figure 1. Comparison of unbound and as captured in the GIF:GM-CSF complex. Alignment of two copies of unbound ovine GM-CSF (slate) with bound GM-CSF in the GIF:GM-CSF complex (GIF: green,
SUPPLEMENTARY INFORMATION
Supplementary Table S1 Kinetic Analyses of the AMSH-LP mutants AMSH-LP K M (μm) k cat x 10-3 (s -1 ) WT 71.8 ± 6.3 860 ± 65.4 T353A 76.8 ± 11.7 46.3 ± 3.7 F355A 58.9 ± 10.4 5.33 ± 0.30 proximal S358A 75.1
SUPPLEMENTARY INFORMATION
Supplementary materials Figure S1 Fusion protein of Sulfolobus solfataricus SRP54 and a signal peptide. a, Expression vector for the fusion protein. The signal peptide of yeast dipeptidyl aminopeptidase
Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Quantitation of the binding of pro53 peptide to sorla Vps10p measured by the AP reporter assay. The graph shows tracings of the typical chromogenic AP reaction observed with AP-pro53
of the Guanine Nucleotide Exchange Factor FARP2
Structure, Volume 21 Supplemental Information Structural Basis for Autoinhibition of the Guanine Nucleotide Exchange Factor FARP2 Xiaojing He, Yi-Chun Kuo, Tyler J. Rosche, and Xuewu Zhang Inventory of
SUPPLEMENTARY INFORMATION
doi:1.138/nature1737 Supplementary Table 1 variant Description FSEC - 2B12 a FSEC - 6A1 a K d (leucine) c Leucine uptake e K (wild-type like) K (Y18F) K (TS) K (TSY) K288A mutant, lipid facing side chain
Supplementary Materials for
www.sciencesignaling.org/cgi/content/full/5/243/ra68/dc1 Supplementary Materials for Superbinder SH2 Domains Act as Antagonists of Cell Signaling Tomonori Kaneko, Haiming Huang, Xuan Cao, Xing Li, Chengjun
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1. Different crystal forms obtained for Sky
Supplementary Figure 1 Different crystal forms obtained for Sky 1 353. (a) Crystal form 1 obtained in the presence of 20% PEG 3350 and 0.2 M ammonium citrate tribasic ph 7.0. (b) Crystal form 1 of the
NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease
University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2009 NMR study of complexes between low molecular mass inhibitors and the West Nile
Nature Structural & Molecular Biology doi: /nsmb Supplementary Figure 1. CRBN binding assay with thalidomide enantiomers.
Supplementary Figure 1 CRBN binding assay with thalidomide enantiomers. (a) Competitive elution assay using thalidomide-immobilized beads coupled with racemic thalidomide. Beads were washed three times
Supplementary Information. The protease GtgE from Salmonella exclusively targets. inactive Rab GTPases
Supplementary Information The protease GtgE from Salmonella exclusively targets inactive Rab GTPases Table of Contents Supplementary Figures... 2 Supplementary Figure 1... 2 Supplementary Figure 2... 3
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Crystallization. a, Crystallization constructs of the ET B receptor are shown, with all of the modifications to the human wild-type the ET B receptor indicated. Residues interacting
Table S1. Primers used for the constructions of recombinant GAL1 and λ5 mutants. GAL1-E74A ccgagcagcgggcggctgtctttcc ggaaagacagccgcccgctgctcgg
SUPPLEMENTAL DATA Table S1. Primers used for the constructions of recombinant GAL1 and λ5 mutants Sense primer (5 to 3 ) Anti-sense primer (5 to 3 ) GAL1 mutants GAL1-E74A ccgagcagcgggcggctgtctttcc ggaaagacagccgcccgctgctcgg
cote cote-yfp spc This work cote cote-yfp spc This work cote cote-yfp spc This work cote cote-yfp spc This work cote cote-yfp spc This work
SUPPLEMENTARY INFORMATION Table S1. List of strains Strains Genotype Source B. subtilis PY79 Prototrophic derivative of B. subtilis 168 (60) RL1070 spovid::kan (12) HS176 cotz phs2 (cotz-gfp spc) (22)
SUPPLEMENTARY INFORMATION
Supplementary Results DNA binding property of the SRA domain was examined by an electrophoresis mobility shift assay (EMSA) using synthesized 12-bp oligonucleotide duplexes containing unmodified, hemi-methylated,
SUPPLEMENTARY INFORMATION. doi: /nature07461
Figure S1 Electrophysiology. a ph-activation of. Two-electrode voltage clamp recordings of Xenopus oocytes expressing in comparison to waterinjected oocytes. Currents were recorded at 40 mv. The ph of
7.012 Problem Set 1 Solutions
ame TA Section 7.012 Problem Set 1 Solutions Your answers to this problem set must be inserted into the large wooden box on wheels outside 68120 by 4:30 PM, Thursday, September 15. Problem sets will not
SUPPLEMENTARY INFORMATION
Fig. 1 Influences of crystal lattice contacts on Pol η structures. a. The dominant lattice contact between two hpol η molecules (silver and gold) in the type 1 crystals. b. A close-up view of the hydrophobic
Supplementary Figure 1. Biochemical and sequence alignment analyses the
Supplementary Figure 1. Biochemical and sequence alignment analyses the interaction of OPTN and TBK1. (a) Analytical gel filtration chromatography analysis of the interaction between TBK1 CTD and OPTN(1-119).
Supporting Information
Supporting Information Mullins et al. 10.1073/pnas.0906781106 SI Text Detection of Calcium Binding by 45 Ca 2 Overlay. The 45 CaCl 2 (1 mci, 37 MBq) was obtained from NEN. The general method of 45 Ca 2
Supporting Information
Supporting Information Ottmann et al. 10.1073/pnas.0907587106 Fig. S1. Primary structure alignment of SBT3 with C5 peptidase from Streptococcus pyogenes. The Matchmaker tool in UCSF Chimera (http:// www.cgl.ucsf.edu/chimera)
Tu 1,*, , Sweden
Supplementary Material Computational studiess of the binding profile of phosphoinositide PtdIns(,4,5)P with the pleckstrin homology domain d of an oomycetee cellulose synthase Guanglin Kuang 1, Vincent
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b).
Supplementary Figure 1 Crystal packing of ClR and electron density maps. Crystal packing of type A crystal (a) and type B crystal (b). Crystal contacts at B-C loop are magnified and stereo view of A-weighted
Any protein that can be labelled by both procedures must be a transmembrane protein.
1. What kind of experimental evidence would indicate that a protein crosses from one side of the membrane to the other? Regions of polypeptide part exposed on the outside of the membrane can be probed
Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets
Supporting information Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Wan-Na Chen, Christoph Nitsche, Kala Bharath Pilla, Bim Graham, Thomas
Table 1. Crystallographic data collection, phasing and refinement statistics. Native Hg soaked Mn soaked 1 Mn soaked 2
Table 1. Crystallographic data collection, phasing and refinement statistics Native Hg soaked Mn soaked 1 Mn soaked 2 Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell
Supplementary figure 1 Application of tmfret in LeuT. (a) To assess the feasibility of using tmfret for distance-dependent measurements in LeuT, a
Supplementary figure 1 Application of tmfret in LeuT. (a) To assess the feasibility of using tmfret for distance-dependent measurements in LeuT, a series of tmfret-pairs comprised of single cysteine mutants
LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor
LS1a Fall 2014 Problem Set #2 Due Monday 10/6 at 6 pm in the drop boxes on the Science Center 2 nd Floor Note: Adequate space is given for each answer. Questions that require a brief explanation should
SUPPLEMENTARY INFORMATION
Dph2 SeMet (iron-free) # Dph2 (iron-free) Dph2-[4Fe-4S] Data collection Space group P2 1 2 1 2 1 P2 1 2 1 2 1 P2 1 2 1 2 1 Cell dimensions a, b, c (Å) 58.26, 82.08, 160.42 58.74, 81.87, 160.01 55.70, 80.53,
Supplementary information
Supplementary information The structural basis of modularity in ECF-type ABC transporters Guus B. Erkens 1,2, Ronnie P-A. Berntsson 1,2, Faizah Fulyani 1,2, Maria Majsnerowska 1,2, Andreja Vujičić-Žagar
SI Text S1 Solution Scattering Data Collection and Analysis. SI references
SI Text S1 Solution Scattering Data Collection and Analysis. The X-ray photon energy was set to 8 kev. The PILATUS hybrid pixel array detector (RIGAKU) was positioned at a distance of 606 mm from the sample.
Structural characterization of NiV N 0 P in solution and in crystal.
Supplementary Figure 1 Structural characterization of NiV N 0 P in solution and in crystal. (a) SAXS analysis of the N 32-383 0 -P 50 complex. The Guinier plot for complex concentrations of 0.55, 1.1,
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Chemical structure of LPS and LPS biogenesis in Gram-negative bacteria. a. Chemical structure of LPS. LPS molecule consists of Lipid A, core oligosaccharide and O-antigen. The polar
Supplementary Figure S1. Urea-mediated buffering mechanism of H. pylori. Gastric urea is funneled to a cytoplasmic urease that is presumably attached
Supplementary Figure S1. Urea-mediated buffering mechanism of H. pylori. Gastric urea is funneled to a cytoplasmic urease that is presumably attached to HpUreI. Urea hydrolysis products 2NH 3 and 1CO 2
List of supplementary data
List of supplementary data Figure S1 Amino acid alignment for GiNT Figure S2Amino acid alignment and phylogenetic analysis for GiGS1 and GiGS2 Figure S3 Amino acid alignment for GiGluS Figure S4 Amino
Expanded View Figures
The EMBO Journal Structure of a Dm peptide bound to the OT module Tobias Raisch et al Expanded View Figures A Hs Dm 262 297 685 8 HEAT HEAT MIF4G 9BD 1SHD 761 91 193 169 1152 1317 16 1376 1467 HEAT HEAT
Structural insights into Aspergillus fumigatus lectin specificity - AFL binding sites are functionally non-equivalent
Acta Cryst. (2015). D71, doi:10.1107/s1399004714026595 Supporting information Volume 71 (2015) Supporting information for article: Structural insights into Aspergillus fumigatus lectin specificity - AFL
Supplementary Figure 3 a. Structural comparison between the two determined structures for the IL 23:MA12 complex. The overall RMSD between the two
Supplementary Figure 1. Biopanningg and clone enrichment of Alphabody binders against human IL 23. Positive clones in i phage ELISA with optical density (OD) 3 times higher than background are shown for
A L A BA M A L A W R E V IE W
A L A BA M A L A W R E V IE W Volume 52 Fall 2000 Number 1 B E F O R E D I S A B I L I T Y C I V I L R I G HT S : C I V I L W A R P E N S I O N S A N D TH E P O L I T I C S O F D I S A B I L I T Y I N
THE CRYSTAL STRUCTURE OF THE SGT1-SKP1 COMPLEX: THE LINK BETWEEN
THE CRYSTAL STRUCTURE OF THE SGT1-SKP1 COMPLEX: THE LINK BETWEEN HSP90 AND BOTH SCF E3 UBIQUITIN LIGASES AND KINETOCHORES Oliver Willhoft, Richard Kerr, Dipali Patel, Wenjuan Zhang, Caezar Al-Jassar, Tina
13-3. Synthesis-Secretory pathway: Sort lumenal proteins, Secrete proteins, Sort membrane proteins
13-3. Synthesis-Secretory pathway: Sort lumenal proteins, Secrete proteins, Sort membrane proteins Molecular sorting: specific budding, vesicular transport, fusion 1. Why is this important? A. Form and
Supplemental Information. Expanded Coverage of the 26S Proteasome. Conformational Landscape Reveals. Mechanisms of Peptidase Gating
Cell Reports, Volume 24 Supplemental Information Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating Markus R. Eisele, Randi G. Reed, Till Rudack, Andreas
Diphthamide biosynthesis requires a radical iron-sulfur enzyme. Pennsylvania State University, University Park, Pennsylvania 16802, USA
Diphthamide biosynthesis requires a radical iron-sulfur enzyme Yang Zhang, 1,4 Xuling Zhu, 1,4 Andrew T. Torelli, 1 Michael Lee, 2 Boris Dzikovski, 1 Rachel Koralewski, 1 Eileen Wang, 1 Jack Freed, 1 Carsten
Protein Sorting, Intracellular Trafficking, and Vesicular Transport
Protein Sorting, Intracellular Trafficking, and Vesicular Transport Noemi Polgar, Ph.D. Department of Anatomy, Biochemistry and Physiology Email: polgar@hawaii.edu Phone: 692-1422 Outline Part 1- Trafficking
SUPPLEMENTARY INFORMATION
www.nature.com/nature 1 Figure S1 Sequence alignment. a Structure based alignment of the plgic of E. chrysanthemi (ELIC), the acetylcholine binding protein from the snail Lymnea stagnalis (AchBP, PDB code
Supplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate
SUPPLEMENTARY FIGURE LEGENDS Supplementary Figure 1. Aligned sequences of yeast IDH1 (top) and IDH2 (bottom) with isocitrate dehydrogenase from Escherichia coli [ICD, pdb 1PB1, Mesecar, A. D., and Koshland,
Cryo-EM data collection, refinement and validation statistics
1 Table S1 Cryo-EM data collection, refinement and validation statistics Data collection and processing CPSF-160 WDR33 (EMDB-7114) (PDB 6BM0) CPSF-160 WDR33 (EMDB-7113) (PDB 6BLY) CPSF-160 WDR33 CPSF-30
SUPPLEMENTARY INFORMATION
Supplementary Table 1: Amplitudes of three current levels. Level 0 (pa) Level 1 (pa) Level 2 (pa) TrkA- TrkH WT 200 K 0.01 ± 0.01 9.5 ± 0.01 18.7 ± 0.03 200 Na * 0.001 ± 0.01 3.9 ± 0.01 12.5 ± 0.03 200
Membrane Protein Channels
Membrane Protein Channels Potassium ions queuing up in the potassium channel Pumps: 1000 s -1 Channels: 1000000 s -1 Pumps & Channels The lipid bilayer of biological membranes is intrinsically impermeable
Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction
Name page 1 of 6 Bahnson Biochemistry Cume, April 8, 2006 The Structural Biology of Signal Transduction Part I. The ion Ca 2+ can function as a 2 nd messenger. Pick a specific signal transduction pathway
Supplementary Information. Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1
Supplementary Information Broad Spectrum Anti-Influenza Agents by Inhibiting Self- Association of Matrix Protein 1 Philip D. Mosier 1, Meng-Jung Chiang 2, Zhengshi Lin 2, Yamei Gao 2, Bashayer Althufairi
JBC Papers in Press. Published on August 13, 2018 as Manuscript RA
JBC Papers in Press. Published on August 13, 2018 as Manuscript RA118.003290 The latest version is at http://www.jbc.org/cgi/doi/10.1074/jbc.ra118.003290 Bond swapping from a charge cloud allows flexible
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11744 Supplementary Table 1. Crystallographic data collection and refinement statistics. Wild-type Se-Met-BcsA-B SmCl 3 -soaked EMTS-soaked Data collection Space
Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08 Å resolution: comparison with the Azotobacter vinelandii MoFe protein
Acta Cryst. (2015). D71, 274-282, doi:10.1107/s1399004714025243 Supporting information Volume 71 (2015) Supporting information for article: Nitrogenase MoFe protein from Clostridium pasteurianum at 1.08
SUPPLEMENTARY INFORMATION
doi:10.1038/nature11054 Supplementary Fig. 1 Sequence alignment of Na v Rh with NaChBac, Na v Ab, and eukaryotic Na v and Ca v homologs. Secondary structural elements of Na v Rh are indicated above the
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION Structure of human carbamoyl phosphate synthetase: deciphering the on/off switch of human ureagenesis Sergio de Cima, Luis M. Polo, Carmen Díez-Fernández, Ana I. Martínez, Javier
Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation
Supplemental Information for: Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion and Orientation Javier L. Baylon, Ivan L. Lenov, Stephen G. Sligar and Emad Tajkhorshid
Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1. MhsT and LeuT architecture.
Supplementary Figure 1 MhsT and LeuT architecture. a, Cartoon structure representation and topology diagram for MhsT in the occluded inward-facing state and b, LeuT in the occluded outward-facing state
Supplementary Figure 1 Schematic overview of ASTNs in neuronal migration. (a) Schematic of roles played by ASTNs 1 and 2. ASTN-1-mediated adhesions
Supplementary Figure 1 Schematic overview of ASTNs in neuronal migration. (a) Schematic of roles played by ASTNs 1 and 2. ASTN-1-mediated adhesions undergo endocytosis into clathrin-coated vesicles dependent
Introduction to the Ribosome Overview of protein synthesis on the ribosome Prof. Anders Liljas
Introduction to the Ribosome Molecular Biophysics Lund University 1 A B C D E F G H I J Genome Protein aa1 aa2 aa3 aa4 aa5 aa6 aa7 aa10 aa9 aa8 aa11 aa12 aa13 a a 14 How is a polypeptide synthesized? 2
RNA Polymerase I Contains a TFIIF-Related DNA-Binding Subcomplex
Molecular Cell, Volume 39 Supplemental Information RNA Polymerase I Contains a TFIIFRelated DNABinding Subcomplex Sebastian R. Geiger, Kristina Lorenzen, Amelie Schreieck, Patrizia Hanecker, Dirk Kostrewa,
Fig. S1. Proliferation and cell cycle exit are affected by the med mutation. (A,B) M-phase nuclei are visualized by a-ph3 labeling in wild-type (A)
Fig. S1. Proliferation and cell cycle exit are affected by the med mutation. (A,B) M-phase nuclei are visualized by a-ph3 labeling in wild-type (A) and mutant (B) 4 dpf retinae. The central retina of the
Molecular Mechanism for Conformational Dynamics of Ras GTP Elucidated from In-Situ Structural Transition in Crystal
Molecular Mechanism for Conformational Dynamics of Ras GTP Elucidated from In-Situ Structural Transition in Crystal Shigeyuki Matsumoto, Nao Miyano, Seiki Baba, Jingling Liao, Takashi Kawamura, Chiemi
Bacterial protease uses distinct thermodynamic signatures for substrate recognition
Bacterial protease uses distinct thermodynamic signatures for substrate recognition Gustavo Arruda Bezerra, Yuko Ohara-Nemoto, Irina Cornaciu, Sofiya Fedosyuk, Guillaume Hoffmann, Adam Round, José A. Márquez,
Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell
Using Higher Calculus to Study Biologically Important Molecules Julie C. Mitchell Mathematics and Biochemistry University of Wisconsin - Madison 0 There Are Many Kinds Of Proteins The word protein comes
References on Kinetics and Mechanisms
References on Kinetics and Mechanisms Excellent reference for all aspects of enzyme kinetics including important elements of Metabolic Control Analysis of relevance to systems analysis of enzyme function
Stabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon
Stabilizing the CH2 domain of an Antibody by Engineering in an Enhanced Aromatic Sequon Wentao Chen,, Leopold Kong, Stephen Connelly, Julia M. Dendle,, Yu Liu,, Ian A. Wilson,#, Evan T. Powers, *, Jeffery
Supplementary Figure 1
A R R RA-selective pocket Cl Adenine pocket and hinge-binding moiety Cl ulfonamide series PLX7 PLX Br BR BR TV PLX RI TQ D RI9 C B PLX7 M ulfonamide concentration Monomer Dimer RA-elective Pocket Unoccupied
Supplemental Information. Molecular Basis of Spectral Diversity. in Near-Infrared Phytochrome-Based. Fluorescent Proteins
Chemistry & Biology, Volume 22 Supplemental Information Molecular Basis of Spectral Diversity in Near-Infrared Phytochrome-Based Fluorescent Proteins Daria M. Shcherbakova, Mikhail Baloban, Sergei Pletnev,
Supplementary Information
Supplementary Information Resveratrol Serves as a Protein-Substrate Interaction Stabilizer in Human SIRT1 Activation Xuben Hou,, David Rooklin, Hao Fang *,,, Yingkai Zhang Department of Medicinal Chemistry
Nature Structural and Molecular Biology: doi: /nsmb.2783
Supplementary Figure 1: Crystallized chimera construct (mhv1cc). (a) Sequence alignment between mhv1cc and other VSDs. These sequences (mhv1cc, Kv1.2 Kv2.1; shaker family voltage gated potassium channel
Experimental and Computational Mutagenesis to Investigate the. Positioning of a General Base within an Enzyme Active Site
Experimental and Computational Mutagenesis to Investigate the Positioning of a General Base within an Enzyme Active Site Jason P. Schwans, Philip Hanoian, Benjamin J. Lengerich, Fanny Sunden, Ana Gonzalez
β1 Structure Prediction and Validation
13 Chapter 2 β1 Structure Prediction and Validation 2.1 Overview Over several years, GPCR prediction methods in the Goddard lab have evolved to keep pace with the changing field of GPCR structure. Despite
Advanced Certificate in Principles in Protein Structure. You will be given a start time with your exam instructions
BIRKBECK COLLEGE (University of London) Advanced Certificate in Principles in Protein Structure MSc Structural Molecular Biology Date: Thursday, 1st September 2011 Time: 3 hours You will be given a start
SPATIAL REGULATION OF EXOCYTOSIS BY RHO FAMILY SMALL GTPASES in Saccharomyces cerevisiae
SPATIAL REGULATION OF EXOCYTOSIS BY RHO FAMILY SMALL GTPASES in Saccharomyces cerevisiae Hao Wu A dissertation submitted to the faculty of the University of North Carolina at Chapel Hill in partial fulfillment
Translation. A ribosome, mrna, and trna.
Translation The basic processes of translation are conserved among prokaryotes and eukaryotes. Prokaryotic Translation A ribosome, mrna, and trna. In the initiation of translation in prokaryotes, the Shine-Dalgarno
Supplementary Information
Supplementary Information An engineered protein antagonist of K-Ras/B-Raf interaction Monique J. Kauke, 1,2 Michael W. Traxlmayr 1,2, Jillian A. Parker 3, Jonathan D. Kiefer 4, Ryan Knihtila 3, John McGee
NB-DNJ/GCase-pH 7.4 NB-DNJ+/GCase-pH 7.4 NB-DNJ+/GCase-pH 4.5
SUPPLEMENTARY TABLES Suppl. Table 1. Protonation states at ph 7.4 and 4.5. Protonation states of titratable residues in GCase at ph 7.4 and 4.5. Histidine: HID, H at δ-nitrogen; HIE, H at ε-nitrogen; HIP,
Supplemental data for
Supplemental data for A Real-Time Guanine Nucleotide Exchange Assay using NMR: Activation of RhoA by PDZ- RhoGEF. Geneviève M.C. Gasmi-Seabrook 1,3, Christopher B. Marshall 1,3, Melissa Cheung 1,3, Bryan
Protein structure. Protein structure. Amino acid residue. Cell communication channel. Bioinformatics Methods
Cell communication channel Bioinformatics Methods Iosif Vaisman Email: ivaisman@gmu.edu SEQUENCE STRUCTURE DNA Sequence Protein Sequence Protein Structure Protein structure ATGAAATTTGGAAACTTCCTTCTCACTTATCAGCCACCT...
Structural insights into energy regulation of light-harvesting complex from spinach CP29
SUPPLEMENTARY INFORMATION Structural insights into energy regulation of light-harvesting complex from spinach CP29 Xiaowei Pan 1, Mei Li 1, Tao Wan 1,2, Longfei Wang 1,2, Chenjun Jia 1,2, Zhiqiang Hou
Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4.
Other Methods for Generating Ions 1. MALDI matrix assisted laser desorption ionization MS 2. Spray ionization techniques 3. Fast atom bombardment 4. Field Desorption 5. MS MS techniques Matrix assisted
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11509 Supplementary Table 1 Data collection and refinement statistics Data collection DmZuc WT DmZuc K171A SeMet-DmZuc WT (residues 41 253) (residues 41 253)
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 14, 2018 02:00 pm GMT PDB ID : 3RRQ Title : Crystal structure of the extracellular domain of human PD-1 Authors : Lazar-Molnar, E.; Ramagopal, U.A.; Nathenson,
What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces: Electronic Supplementary
Electronic Supplementary Material (ESI) for Journal of Materials Chemistry B. This journal is The Royal Society of Chemistry 21 What makes a good graphene-binding peptide? Adsorption of amino acids and
Esser et al. Crystal Structures of R. sphaeroides bc 1
Esser et al. Crystal Structures of R. sphaeroides bc Supplementary Information Trivariate Gaussian Probability Analysis The superposition of six structures results in sextets of 3D coordinates for every
Way to impose membrane curvature
Way to impose membrane curvature Sar1 reticulons? clathrin and other vesicle coats dynamin BAR domains McMahon, 2005 The ER is continuous with the nuclear envelope and contains tubules and sheets Gia Voeltz
7.012 Problem Set 1. i) What are two main differences between prokaryotic cells and eukaryotic cells?
ame 7.01 Problem Set 1 Section Question 1 a) What are the four major types of biological molecules discussed in lecture? Give one important function of each type of biological molecule in the cell? b)
Structural basis for catalytically restrictive dynamics of a high-energy enzyme state
Supplementary Material Structural basis for catalytically restrictive dynamics of a high-energy enzyme state Michael Kovermann, Jörgen Ådén, Christin Grundström, A. Elisabeth Sauer-Eriksson, Uwe H. Sauer
Model Mélange. Physical Models of Peptides and Proteins
Model Mélange Physical Models of Peptides and Proteins In the Model Mélange activity, you will visit four different stations each featuring a variety of different physical models of peptides or proteins.
Cyclical Regulation of the Exocyst and Cell Polarity Determinants for Polarized Cell Growth
Molecular Biology of the Cell Vol. 16, 1500 1512, March 2005 Cyclical Regulation of the Exocyst and Cell Polarity Determinants for Polarized Cell Growth Allison Zajac,* Xiaoli Sun,* Jian Zhang, and Wei
Nature Structural & Molecular Biology: doi: /nsmb.3343
Supplementary Figure 1 Sequence alignment for PC2 and related orthologs. The sequence of human PC2 P185-D723 (hspc2; TRPP1) is shown along with the corresponding PC2 sequences from C. elegans (ce) and
Supplemental Data SUPPLEMENTAL FIGURES
Supplemental Data CRYSTAL STRUCTURE OF THE MG.ADP-INHIBITED STATE OF THE YEAST F 1 C 10 ATP SYNTHASE Alain Dautant*, Jean Velours and Marie-France Giraud* From Université Bordeaux 2, CNRS; Institut de
Supplementary Figures
1 Supplementary Figures Supplementary Figure 1 Type I FGFR1 inhibitors (a) Chemical structures of a pyrazolylaminopyrimidine inhibitor (henceforth referred to as PAPI; PDB-code of the FGFR1-PAPI complex: