Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1
|
|
|
- Earl Rose
- 5 years ago
- Views:
Transcription
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 (orange) or control AP-MycHis (blue) eluted from the sorla Vps10p-beads. Note that gradual increase in the absorbance with the AP-MycHis is indistinguishable from that with mock sample (where no AP activity is present in the reaction mixture), indicating that the background nonspecific binding of AP protein to the beads is negligible.
2 Supplementary Figure 2 Sequence alignment of the Vps10p domains. Amino acid sequences are from human sorla (SORLA_hu, NP_ ), human sortilin (sort_hu, CCA66904), mouse SorCS1 (sorcs1_mo, Q9JLC4), and yeast Vps10p (Vps10p_sp, O42930). Secondary structure elements are denoted by straight (strands) or wavy (helices) lines below each sequence. Strand designation is shown above the alignment with the same color code as in Fig. 3. The L1 and L2 segments are highlighted in salmon and cyan, respectively. Cysteines are shown with a grey background with lines connecting the disulfide-bonded pair. The Gly511 mutated in a familial AD patient is marked by a red box. Propeptide cleavage sites are indicated by //.
3 Supplementary Figure 3 Close-up view of the propeptide-binding site in the propeller tunnel. The Vps10p propeller domain (gray) is shown in surface (left) or ribbon (right) presentations, with L1, L2, and the AD-causing mutation residue Gly511 colored in salmon, cyan, and red, respectively. Propeptide ligand bound inside the tunnel is shown in CPK model in both panels.
4 Supplementary Figure 4
5 Residue-wise conformational flexibility of the sorla Vps10p domain. (a) Structural changes that accompany propeptide binding. The residue number is plotted against distance between mainchain Cα atoms in the ligand-free (at ph 4.5) and the propeptide-bound (at ph 6.5) forms of the sorla Vps10p domain after structural superposition. Regions disordered in either structure are indicated by horizontal light blue bars. Note that the largest structural differences are found in L1 and the 10CC-b segments. (b) RMSF values for each residue during the MD simulation of the propeptidebound form of sorla Vps10p domain (see the legend to Figure 5d) are plotted similarly to the (a).
6 Supplementary Figure 5 Prediction of β-aggregation tendency of various sorla Vps10p ligand peptides with the PASTA server. The amino acid sequencse of (a) the sorla propeptide (53 residues), (b) Aβ40 (40 residues), (c) NT (13 residues), (d) HA (11 residues), and the sortilin propeptide (44 residues) were fed to the PASTA server ( and the resultant per-residue aggregation probability scores, h(k), are plotted.
7 Supplementary Table 1 Affinity values of sorla Vps10p domain toward various peptides/ligands. Ligand Receptor Format K D Reference GST-sortilin pro (1-44) sorla Vps10p BIAcore 5-15 nm* [17] GST-sorLA pro (1-53) sorla Vps10p BIAcore 47 nm* [50] GST-sorLA pro (19-38) sorla Vps10p BIAcore 150 nm* [50] β-vldl(apoe-rich) FL sorla on KT38 cells radioligand assay 28 µg/ml** [3] PDGF-BB FL sorla BIAcore 10 nm*** [51] HA (bipeptide) unpurified sorla Vps10p radioligand Scatchard analysis 1.3 nm* [52] HA (monomer) sorla Vps10p BIAcore ~500 nm [17] sorla pro sorla Vps10p FP 441 nm this study Aβ40 sorla Vps10p FP 235 nm this study Aβ 6-20 sorla Vps10p FP 692 nm this study NT sorla Vps10p FP 1.0 µm this study * Because of the bivalent nature of the ligand (either GST-fusion or crosslinked peptide), these values are overestimated. ** ~100nM assuming that β-ldl is equal to one apoe chain of 30 kda. Likely to be mediated by the LA region rather than the Vps10p domain. *** Not mediated by the Vps10p domain Supplementary References [50] U.B. Westergaard, E.S. Sorensen, G. Hermey, M.S. Nielsen, A. Nykjaer, K. Kirkegaard, C. Jacobsen, J. Gliemann, P. Madsen, C.M. Petersen, Functional organization of the sortilin Vps10p domain. J Biol Chem 279 (2004) [51] J. Gliemann, G. Hermey, A. Nykjaer, C.M. Petersen, C. Jacobsen, P.A. Andreasen, The mosaic receptor sorla/lr11 binds components of the plasminogen-activating system and platelet-derived growth factor-bb similarly to LRP1 (low-density lipoprotein receptor-related protein), but mediates slow internalization of bound ligand. Biochem J 381 (2004) [52] J. Lintzel, I. Franke, I.B. Riedel, H.C. Schaller, W. Hampe, Characterization of the VPS10 domain of SorLA/LR11 as binding site for the neuropeptide HA. Biol Chem 383 (2002)
8 Supplementary Table 2. Binding of various peptide-ap fusion proteins to the sorla Vps10p domain. Construct Sequence Bound AP activity (%) a AP-mycHis AP-13aa-EALSLEGPEQKLISEEDLNSAVDHHHHHH 1.6 ± 0.6 AP-pro53 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQGDPRELRLWARGDARGASRADEKPLRRKR 100 AP-Aβ 1-32 AP-13aa-DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAII 78 ± 6.7 AP-NT AP-15aa-ELYENKPRRPYIL 1.1 ± 0.4 AP-HA AP-15aa-QPPGGSKVILF 1.1 ± 0.4 AP-SORTpropeptide AP-15aa-QDRLDAPPPPAAPLPRWSGPIGVSWGLRAAAAGGAFPRGGRWRR 5.8 ± 0.7 AP-BACEpropeptide AP-15aa-TQHGIRLPLRSGLGGAPLGLRLP 1.1 ± 0.3 a AP activities associated with the sorla Vps10p-coated beads are expressed as percent of the value obtained with C-terminally fused pro53 (n=3; mean ± s.d.).
9 Supplementary Table 3. Binding of various mutant sorla propeptides to sorla Vps10p. Construct Sequence Bound AP activity (%) a N-terminal fusion AP-pro53 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQGDPRELRLWARGDARGASRADEKPLRRKR 100 AP-pro28 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQGDPR 103 ± 5.3 AP-pro26 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQGD 76 ± 8.0 AP-pro25 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQG 146 ± 26 AP-pro24 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVVQ 602 ± 121 AP-pro23 AP-13aa-EVWTQRLHGGSAPLPQDRGFLVV 2.8 ± 1.6 AP-pro53(G19A) AP-13aa A ± 1.8 AP-pro53(F20A) AP-13aa A ± 0.4 AP-pro53(L21A) AP-13aa A ± 48 AP-pro53(V22A) AP-13aa A ± 6.8 AP-pro53(V23A) AP-13aa A ± 0.8 AP-pro53(Q24A) AP-13aa A ± 7.0 AP-pro53(G25A) AP-13aa A ± 34 C-terminal fusion pro49-ap EVWTQRLHGGSAPLPQDRGFLVVQGDPRELRLWARGDARGASRADEKPL-4aa-AP 354 ± 26 pro49-ap(g19a) A aa-AP 10 ± 1.5 pro49-ap(g25a) A aa-AP 457 ± 50 a AP activities associated with the sorla Vps10p-coated beads are expressed as percent of the value obtained with C-terminally fused pro53 (n=3; mean ± s.d.).
10 Supplementary Table 4. Binding of various mutant Aβ peptides to sorla Vps10p. Construct Sequence Bound AP activity (%) a AP-Aβ 1-40 AP-13aa-DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV N.D. AP-Aβ 1-32 AP-13aa-DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAII 117 ± 5.8 AP-Aβ 1-22 AP-13aa-DAEFRHDSGYEVHHQKLVFFAE 42 ± 6.7 AP-Aβ 1-16 AP-13aa-DAEFRHDSGYEVHHQK 0.2 ± 0.1 AP-Aβ 1-22 (G9A) AP-13aa A ± 1.2 AP-Aβ 1-22 (Y10A) AP-13aa A ± 0.2 AP-Aβ 1-22 (E11A) AP-13aa A ± 2.9 AP-Aβ 1-22 (V12A) AP-13aa A ± 5.7 AP-Aβ 1-22 (H13A) AP-13aa A ± 0.2 AP-Aβ 1-22 (H14A) AP-13aa A ± 1.9 AP-Aβ 1-22 (Q15A) AP-13aa A ± 2.5 AP-Aβ 1-22 (K16A) AP-13aa A N.D. AP-Aβ 1-22 (L17A) AP-13aa A ± 5.4 AP-Aβ 1-22 (V18A) AP-13aa A ± 0.1 AP-Aβ 1-22 (F19A) AP-13aa A ± 0.2 AP-Aβ 1-22 (F20A) AP-13aa A ± 0.1 a AP activities associated with the sorla Vps10p-coated beads are expressed as percent of the value obtained with C-terminally fused pro53 (n=3; mean ± s.d.). N.D., not determined because the AP-fusion proteins were not secreted into the medium by the transfected cells.
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
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 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).
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
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
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 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
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
Supplemental Information. The Mitochondrial Fission Receptor MiD51. Requires ADP as a Cofactor
Structure, Volume 22 Supplemental Information The Mitochondrial Fission Receptor MiD51 Requires ADP as a Cofactor Oliver C. Losón, Raymond Liu, Michael E. Rome, Shuxia Meng, Jens T. Kaiser, Shu-ou Shan,
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
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1.
Table S1. Overview of used PDZK1 constructs and their binding affinities to peptides. Related to figure 1. PDZK1 constru cts Amino acids MW [kda] KD [μm] PEPT2-CT- FITC KD [μm] NHE3-CT- FITC KD [μm] PDZK1-CT-
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,
Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions. Implicated in Dimerization and Autoinhibition
JBC Papers in Press. Published on November 1, 2000 as Manuscript M006502200 Crystal Structure of Fibroblast Growth Factor 9 (FGF9) Reveals Regions Implicated in Dimerization and Autoinhibition 1 Copyright
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R)
Supplementary Figure 1 Crystal contacts in COP apo structure (PDB code 3S0R) Shown in cyan and green are two adjacent tetramers from the crystallographic lattice of COP, forming the only unique inter-tetramer
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,
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. 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
Rho1 binding site PtdIns(4,5)P2 binding site Both sites
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
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
doi:10.1038/nature10955 Supplementary Figures Supplementary Figure 1. Electron-density maps and crystallographic dimer structures of the motor domain. (a f) Stereo views of the final electron-density maps
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 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
Cks1 CDK1 CDK1 CDK1 CKS1. are ice- lobe. conserved. conserved
Cks1 d CKS1 Supplementary Figure 1 The -Cks1 crystal lattice. (a) Schematic of the - Cks1 crystal lattice. -Cks1 crystallizes in a lattice that contains c 4 copies of the t - Cks1 dimer in the crystallographic
SUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Supplementary Figure 1 Protein sequence alignment of Vibrionaceae with either a 40-residue insertion or a 44-residue insertion. Identical residues are indicated by red background.
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Identification of the ScDcp2 minimal region interacting with both ScDcp1 and the ScEdc3 LSm domain. Pull-down experiment of untagged ScEdc3 LSm with various ScDcp1-Dcp2-His 6 fragments.
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
Supplementary Figure 1. SDS-PAGE analysis of GFP oligomer variants with different linkers. Oligomer mixtures were applied to a PAGE gel containing
Supplementary Figure 1. SDS-PAGE analysis of GFP oligomer variants with different linkers. Oligomer mixtures were applied to a PAGE gel containing 0.1% SDS without boiling. The gel was analyzed by a fluorescent
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
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,
Protein Structure. W. M. Grogan, Ph.D. OBJECTIVES
Protein Structure W. M. Grogan, Ph.D. OBJECTIVES 1. Describe the structure and characteristic properties of typical proteins. 2. List and describe the four levels of structure found in proteins. 3. Relate
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 INFORMATION
Figure S1. Secondary structure of CAP (in the camp 2 -bound state) 10. α-helices are shown as cylinders and β- strands as arrows. Labeling of secondary structure is indicated. CDB, DBD and the hinge are
Nature Structural and Molecular Biology: doi: /nsmb Supplementary Figure 1. Definition and assessment of ciap1 constructs.
Supplementary Figure 1 Definition and assessment of ciap1 constructs. (a) ciap1 constructs used in this study are shown as primary structure schematics with domains colored as in the main text. Mutations
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
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)
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 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,
Conformational Geometry of Peptides and Proteins:
Conformational Geometry of Peptides and Proteins: Before discussing secondary structure, it is important to appreciate the conformational plasticity of proteins. Each residue in a polypeptide has three
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.
Programme Last week s quiz results + Summary Fold recognition Break Exercise: Modelling remote homologues
Programme 8.00-8.20 Last week s quiz results + Summary 8.20-9.00 Fold recognition 9.00-9.15 Break 9.15-11.20 Exercise: Modelling remote homologues 11.20-11.40 Summary & discussion 11.40-12.00 Quiz 1 Feedback
Modeling for 3D structure prediction
Modeling for 3D structure prediction What is a predicted structure? A structure that is constructed using as the sole source of information data obtained from computer based data-mining. However, mixing
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
Protein Structure Basics
Protein Structure Basics Presented by Alison Fraser, Christine Lee, Pradhuman Jhala, Corban Rivera Importance of Proteins Muscle structure depends on protein-protein interactions Transport across membranes
Supplemental Data. Gao et al. (2012). Plant Cell /tpc
Supplemental Figure 1. Plant EMP Proteins. (A) The Accession numbers of the 12 EMP members from Arabidopsis. (B) Phylogenetic analysis of EMP proteins from Arabidopsis, human and yeast using the Mac Vector
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. Structural basis for precursor protein-directed ribosomal peptide macrocyclization
Supplementary Information Structural basis for precursor protein-directed ribosomal peptide macrocyclization Kunhua Li 1,3, Heather L. Condurso 1,3, Gengnan Li 1, Yousong Ding 2 and Steven D. Bruner 1*
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
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
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 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
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
CH 3 CH 2 OH +H 2 O CHO. 2e + 2H + + O 2 H 2 O +HCOOH
2 4 H CH 3 2e + 2H + + 2 H 2 2 H CH 2 H 2e + 2H + + 2 H 2 2 H +H 2 CH 2e + 2H + + 2 H 2 2 H +HCH Supplemental Figure S. The three-step 4DM reaction, each step requires two reducing equivalents from ADPH
Analysis of nucleotide binding to p97 reveals the properties of a tandem AAA hexameric ATPase
SUPPLEMENTARY INFORMATION Analysis of nucleotide binding to p97 reveals the properties of a tandem AAA hexameric ATPase Louise C Briggs, Geoff S Baldwin, Non Miyata, Hisao Kondo, Xiaodong Zhang, Paul S
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
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
Structural and mechanistic insight into the substrate. binding from the conformational dynamics in apo. and substrate-bound DapE enzyme
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 215 Structural and mechanistic insight into the substrate binding from the conformational
Time-dependence of key H-bond/electrostatic interaction distances in the sirna5-hago2 complexes... Page S14
Supporting Information Probing the Binding Interactions between Chemically Modified sirnas and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations S. Harikrishna* and P. I. Pradeepkumar*
Acta Crystallographica Section D
Supporting information Acta Crystallographica Section D Volume 70 (2014) Supporting information for article: Structural characterization of the virulence factor Nuclease A from Streptococcus agalactiae
Supporting Information
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2016 Supporting Information Lipid molecules can induce an opening of membrane-facing
Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6
Supplementary Information for: Lipid Regulated Intramolecular Conformational Dynamics of SNARE-Protein Ykt6 Yawei Dai 1, 2, Markus Seeger 3, Jingwei Weng 4, Song Song 1, 2, Wenning Wang 4, Yan-Wen 1, 2,
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
Supporting Information
Supporting Information Superagonist, Full Agonist, Partial Agonist and Antagonist Actions of Arylguanidines at 5-Hydroxytryptamine-3 (5-HT 3 ) Subunit A Receptors Katie Alix, Shailesh Khatri, Philip D.
type GroEL-GroES complex. Crystals were grown in buffer D (100 mm HEPES, ph 7.5,
Supplementary Material Supplementary Materials and Methods Structure Determination of SR1-GroES-ADP AlF x SR1-GroES-ADP AlF x was purified as described in Materials and Methods for the wild type GroEL-GroES
Supplementary Information
1 Supplementary Information Figure S1 The V=0.5 Harker section of an anomalous difference Patterson map calculated using diffraction data from the NNQQNY crystal at 1.3 Å resolution. The position of the
Supplementary Information. Overlap between folding and functional energy landscapes for. adenylate kinase conformational change
Supplementary Information Overlap between folding and functional energy landscapes for adenylate kinase conformational change by Ulrika Olsson & Magnus Wolf-Watz Contents: 1. Supplementary Note 2. Supplementary
Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS
Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS CNS input file generatemetal.inp: remarks file generate/generatemetal.inp
The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel
SUPPORTING INFORMATION The structure of the deubiquitinase USP15 reveals a misaligned catalytic triad and an open ubiquitin-binding channel Stephanie J. Ward, Hayley E. Gratton, Peni Indrayudha #, Camille
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
Nature Structural & Molecular Biology: doi: /nsmb Supplementary Figure 1
Supplementary Figure 1 Zn 2+ -binding sites in USP18. (a) The two molecules of USP18 present in the asymmetric unit are shown. Chain A is shown in blue, chain B in green. Bound Zn 2+ ions are shown as
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,
Viewing and Analyzing Proteins, Ligands and their Complexes 2
2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing
Structure of the SPRY domain of human DDX1 helicase, a putative interaction platform within a DEAD-box protein
Supporting information Volume 71 (2015) Supporting information for article: Structure of the SPRY domain of human DDX1 helicase, a putative interaction platform within a DEAD-box protein Julian Kellner
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
Destruction of Amyloid Fibrils by Graphene through Penetration and Extraction of Peptides
Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2015 Destruction of Amyloid Fibrils by Graphene through Penetration and Extraction of Peptides Zaixing
Supplementary Figures. Measuring Similarity Between Dynamic Ensembles of Biomolecules
Supplementary Figures Measuring Similarity Between Dynamic Ensembles of Biomolecules Shan Yang, Loïc Salmon 2, and Hashim M. Al-Hashimi 3*. Department of Chemistry, University of Michigan, Ann Arbor, MI,
The Fic protein Doc uses an inverted substrate to phosphorylate and. inactivate EF-Tu
The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu Daniel Castro-Roa 1, Abel Garcia-Pino 2,3 *, Steven De Gieter 2,3, Nico A.J. van Nuland 2,3, Remy Loris 2,3, Nikolay
Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits. AhpC and AhpF from Escherichia coli
Structure, mechanism and ensemble formation of the Alkylhydroperoxide Reductase subunits AhpC and AhpF from Escherichia coli Phat Vinh Dip 1,#, Neelagandan Kamariah 2,#, Malathy Sony Subramanian Manimekalai
SUPPLEMENTARY MATERIAL FOR
SUPPLEMENTARY MATERIAL FOR THE LIPID-BINDING DOMAIN OF WILD TYPE AND MUTANT ALPHA- SYNUCLEIN: COMPACTNESS AND INTERCONVERSION BETWEEN THE BROKEN- AND EXTENDED-HELIX FORMS. Elka R. Georgieva 1, Trudy F.
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
Interpreting and evaluating biological NMR in the literature. Worksheet 1
Interpreting and evaluating biological NMR in the literature Worksheet 1 1D NMR spectra Application of RF pulses of specified lengths and frequencies can make certain nuclei detectable We can selectively
THE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION
THE TANGO ALGORITHM: SECONDARY STRUCTURE PROPENSITIES, STATISTICAL MECHANICS APPROXIMATION AND CALIBRATION Calculation of turn and beta intrinsic propensities. A statistical analysis of a protein structure
Supplemental Information
Supplemental Information Combinatorial Readout of Unmodified H3R2 and Acetylated H3K14 by the Tandem PHD Finger of MOZ Reveals a Regulatory Mechanism for HOXA9 Transcription Yu Qiu 1, Lei Liu 1, Chen Zhao
Exam I Answer Key: Summer 2006, Semester C
1. Which of the following tripeptides would migrate most rapidly towards the negative electrode if electrophoresis is carried out at ph 3.0? a. gly-gly-gly b. glu-glu-asp c. lys-glu-lys d. val-asn-lys
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,
Useful background reading
Overview of lecture * General comment on peptide bond * Discussion of backbone dihedral angles * Discussion of Ramachandran plots * Description of helix types. * Description of structures * NMR patterns
SUPPLEMENTARY EXPERIMENTAL PROCEDURES
SUPPLEMENTARY EXPERIMENTAL PROCEDURES Yeast two-hybrid assay The yeast two hybrid assay was performed according to described in Assmann (2006) [01] and was performed with the baits SCOCO (2-82) and SCOCO
Supporting Information
Supporting Information Oxaliplatin binding to human copper chaperone Atox1 and protein dimerization Benny D. Belviso, 1 Angela Galliani, 2 Alessia Lasorsa, 2 Valentina Mirabelli, 1,3 Rocco Caliandro, 1
CHAPTER 1 THE STRUCTURAL BIOLOGY OF THE FGF19 SUBFAMILY
CHAPTER 1 THE STRUCTURAL BIOLOGY OF THE FGF19 SUBFAMILY Andrew Beenken and Moosa Mohammadi* Department of Pharmacology, New York University School of Medicine, New York, New York, USA. *Corresponding Author:
Values are straight multiplications of WT affinities, so that 25 x WT is weaker binding and ½ WT is tighter binding. IPTG ph 7.4. IPTG ph 9.
1 of 6 10/9/2012 1:05 PM nown functional effects of mutating hypothesized charged residues. Values are straight multiplications of WT affinities, so that 25 x WT is weaker binding and ½ WT is tighter binding.
SUPPLEMENTARY INFORMATION
doi:10.1038/nature17991 Supplementary Discussion Structural comparison with E. coli EmrE The DMT superfamily includes a wide variety of transporters with 4-10 TM segments 1. Since the subfamilies of the
A Single Outer Sphere Mutation Stabilizes apo- Mn Superoxide Dismutase by 35 C and. Disfavors Mn Binding.
Supporting information for A Single Outer Sphere Mutation Stabilizes apo- Mn Superoxide Dismutase by 35 C and Disfavors Mn Binding. Anne-Frances Miller* and Ting Wang Department of Chemistry, University
Supporting information for
Supporting information for Rewiring multi-domain protein switches: transforming a fluorescent Zn 2+ -sensor into a light-responsive Zn 2+ binding protein Stijn J.A. Aper and Maarten Merkx Laboratory of
Secondary and sidechain structures
Lecture 2 Secondary and sidechain structures James Chou BCMP201 Spring 2008 Images from Petsko & Ringe, Protein Structure and Function. Branden & Tooze, Introduction to Protein Structure. Richardson, J.
We used the PSI-BLAST program (http://www.ncbi.nlm.nih.gov/blast/) to search the
SUPPLEMENTARY METHODS - in silico protein analysis We used the PSI-BLAST program (http://www.ncbi.nlm.nih.gov/blast/) to search the Protein Data Bank (PDB, http://www.rcsb.org/pdb/) and the NCBI non-redundant
Gürol M. Süel, Steve W. Lockless, Mark A. Wall, and Rama Ra
Gürol M. Süel, Steve W. Lockless, Mark A. Wall, and Rama Ranganathan, Evolutionarily conserved networks of residues mediate allosteric communication in proteins, Nature Structural Biology, vol. 10, no.
Supporting Information
Supporting Information Arai et al. 10.1073/pnas.15179911 SI Text Protein Expression and Purification. Myb3 (mouse, residues 84 315) was expressed in Escherichia coli as a fusion with the B1 domain of protein
From the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences,16/10 Miklukho- Maklaya Street, Moscow, Russia;
Supplementary information High-Affinity α-conotoxin PnIA Analogs Designed on the Basis of Protein Surface Topography Method Igor E. Kasheverov 1*, Anton O. Chugunov 1*, Denis S. Kudryavtsev 1, Igor A.
Supplementary Materials for
advances.sciencemag.org/cgi/content/full/1/9/e1500511/dc1 Supplementary Materials for Contractility parameters of human -cardiac myosin with the hypertrophic cardiomyopathy mutation R403Q show loss of
Supporting Information
Supporting Information Allosteric communication disrupted by small molecule binding to the Imidazole glycerol phosphate synthase protein-protein interface. Ivan Rivalta*,#, George P. Lisi #, Ning-Shiuan
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,