Esser et al. Crystal Structures of R. sphaeroides bc 1
|
|
- Corey Wilkinson
- 6 years ago
- Views:
Transcription
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 atom position. In the following, the analysis was restricted to Cα atoms representing the loci of the amino acids. If, in general, the positions of a set of atoms were governed only by un-correlated, random errors (as expected for instance of errors within the x-ray diffraction derived coordinates), the distributions around the mean of a sextet three coordinates (x,y,z) would be approximately equal (Esser et al., 2004). In a Gaussian analysis, this would result in a sphere with a volume that when plotted, represents a userselected probability (integrated probability density) of finding an atom inside the sphere. Conversely, non-random or correlated coordinate changes lead eventually to ellipsoids whose longest principal axes indicates the direction of highest positional spread ( motion ). Given three chance variables, x, y, z, and S, which is a region in x, y, z space, the probability of finding S (probability of locating an atom) inside a volume is defined p(s) = ### "(x, y,z)dxdydz = ### "( x r )dx r Volume Volume, where "(x, y,z) is the probability density function (Burnett and Johnson, 996). For trivariate Gaussian distribution, ( x % x ˆ ) T M % ( x r % x ˆ ) "( r x ) = and M is the variance covariance matrix, (2# ) 3/2 $ M e% 2 $ r " v xx v xy v xz % $ ' M = v yx v yy v yz $ # v zx v zy v ' zz &. The v xx, v xy, v xz, v yy, v yz, v zz are variance and co-variance, which are calculated based on, where xˆ = N! x i i= v xy N = # i= ( x! xˆ )( " y! yˆ ) i. For this case, N is the number of contributors (here N=6). i,
2 Esser et al. Crystal Structures of R. sphaeroides bc Principal axes for the probability ellipsoid are determined following a coordinate transformation (new coordinate system x, y, z ) that reduces the cross terms to zero, which is done by an Eigenvector analysis. The transformed M matrix takes the following form " % $ v 0 0 x' x' ' M = $ 0 v 0 ' y' y' $ 0 0 v ' # z'z' &. Consequently, the probability density function after the coordinate transformation becomes where "(x',y',z' ) = U 2 = (x' " x ˆ ')2 + (y' " y ˆ ')2 + (z' " z ˆ ') # x' & (2#) 3/2 e 2 $U 2 $% $% $% x' y' z' # y' # z', The" 2 x'," 2 2 y'," z' are the variances along the principal axes. The normal probability density function is constant for points on the ellipsoid with the value U. To relate U to a probability one needs to solve the equation (here in spherical coordinates): The following tabulates the value of P versus U that can be obtained from mathematical handbooks. P(U) = U 2 " # r2 % r22 $ # e dr 0 P (probability) U
3 Esser et al. Crystal Structures of R. sphaeroides bc The program Mudi has been written in house that performs the multi (=tri) variate Gaussian analysis (available upon request: It reads superimposed pdb files and writes out arrays of eigenvectors and eigenvalues and appropriate instructions for povray ( Supplementary Figures Figure S Interaction of ISP and cyt c at the periplasmic side of the membrane. Extra lateral support of ISP is provided in Rsbc by the insertion from 60 to 80, which features a disulfide bridge: Cys 69 to Cys 45. In mitochondrial bc, subunit VIII is spatially close and can provide shielding for ISP against the lipid and/or aqueous phase. Cyan (Rsbc ) and magenta (Btbc ) surfaces show spatial overlap in the vicinity of ISP. ISP in light gray is a model of the c -state and the yellow trace outlines the observed position of ISP in Rsbc. The red insertion (97-08) into ISP remains distal to the cyt c heme. Supplementary Tables Table S Distances (Å) between iron atoms in prosthetic groups in dimeric bc complexes. Table S2 Hydrogen bonding network at the cytoplasmic side. Table S3 H-bonding network of Rsbc ISP insertion compared to Rcbc ISP insertion Supplementary References: 3
4 Esser et al. Crystal Structures of R. sphaeroides bc Burnett, M. and Johnson, C.K. (996) ORTEP-III. Oak Ridge Thermal Ellipsoid Plot Program For Crystal Structure Illustrations. In ORNL-6895, O.R.N.L.R. (ed.). Oak Ridge National Lab. Esser, L., Quinn, B., Li, Y., Zhang, M., Elberry, M., Yu, L., Yu, C.A. and Xia, D. (2004) Crystallographic studies of quinol oxidation site inhibitors: A modified classification of inhibitors for the cytochrome bc complex. Journal of Molecular Biology, 34,
5 Esser et al., Figure S
6 Table S Distances (Å) between iron atoms in prosthetic groups in dimeric bc complexes. Species a Prosthetic group pairs Rsbc Bovine Yeast Alga (b 6 f) b L - b H b L - 2Fe2S b 2Fe2S - c b H - b H c b H - b L c b L - b L c Rmsd (RS) d b L, b L, b H, b H a Distances were obtained from the following PDB files: Bovine; SQX, Yeast; EZV, and Alga; Q90. b Cytochrome f in the case of b 6 f. c Distance between irons in two-fold symmetry related prosthetic groups. d Rms deviation between different species and Rsbc.
7 Table S2 Hydrogen bonding network at the cytoplasmic side. cyt b C-terminal residues. Atom Atom H bonding partner in cyt b Distance [Ǻ] Asp 420 (i helix) OD HN Glu 425 (i helix) 2.90 Asp 420 (i helix) OD2 HN Arg 230 (de helix) 2.88 Glu 425 (i helix) OE2 NH Arg 230 (de helix) 2.67 Asp 427 (i helix) OD NH Arg 358 (pre-g helix) a 3.63 Ile 424 (i helix) HN O Glu 228 (de helix) b 4.70 Arg 23 (de helix) NH2 O Thr 29 (pre-de helix) 3.59 b H (propionate) OD HN Asn 222 (pre-de helix) 3.03 Glu 228 OE NH2 Arg a H-bond to observed phospholipids. b Potential for an H-bond.
8 Table S3 H-bonding network of Rsbc ISP insertion compared to Rcbc ISP insertion Rhodobacter Sphaeroides Rhodobacter Capsulatus Res Atm Atm 2 Res 2 Dist [Ǻ] Res Atm Atm 2 Res 2 Dist [Ǻ] Asp 95 OD N Asn Asp 95 OD N Ser Asp 95 OD2 NE Arg Asp 95 OD2 OE Glu Thr 96 O N Ala Thr 96 O N Ala Asn 97 ND2 O Ala Ser 97 OG O Ala a Asn 97 ND2 O Ala N/A Asn 97 O ND2 Asn a Ser 97 O ND2 Asn a Ala 98 N O Ala Ala 98 N O Ala Arg 99 NE OD2 Asp Glu 99 OE2 OD Asp Arg 99 cen b cen b Glu Glu 99 cen b cen b Arg 73 ~5.8 Ala 0 N O Ile Ala 0 N O Ile Asn 02 OD N Ala Asn 02 OD N Ala Asn 02 ND2 O Pro Asn 02 ND2 O Pro 78 ~5.29 Asp 04 OD2 N Gly N/A Glu 08 N OD Asn 3 3. c Glu 07 N OD Asn c a Rc Ser 97 -Ala 98 exhibits a flipped peptide relative to the equivalent Rs Asn 97 -Ala 98. b Center of gravity between two charged groups. Coplanar functional groups (no H-bond) but charge interaction possible (Rs Glu69 spatially corresponds to Rc Arg 73. c Rc Asn 2 adopts a non-equivalent position relative to Rs Asn 3.
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
More information1. What is an ångstrom unit, and why is it used to describe molecular structures?
1. What is an ångstrom unit, and why is it used to describe molecular structures? The ångstrom unit is a unit of distance suitable for measuring atomic scale objects. 1 ångstrom (Å) = 1 10-10 m. The diameter
More informationSupplementary 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
More informationStructure 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
More informationFigure 1. Molecules geometries of 5021 and Each neutral group in CHARMM topology was grouped in dash circle.
Project I Chemistry 8021, Spring 2005/2/23 This document was turned in by a student as a homework paper. 1. Methods First, the cartesian coordinates of 5021 and 8021 molecules (Fig. 1) are generated, in
More informationSupplementary 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,
More informationA DARK GREY P O N T, with a Switch Tail, and a small Star on the Forehead. Any
Y Y Y X X «/ YY Y Y ««Y x ) & \ & & } # Y \#$& / Y Y X» \\ / X X X x & Y Y X «q «z \x» = q Y # % \ & [ & Z \ & { + % ) / / «q zy» / & / / / & x x X / % % ) Y x X Y $ Z % Y Y x x } / % «] «] # z» & Y X»
More informationModel 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.
More informationStructure at 2.3 Å resolution of the cytochrome bc 1
Research Article 669 Structure at 2.3 Å resolution of the cytochrome complex from the yeast Saccharomyces cerevisiae co-crystallized with an antibody Fv fragment Carola Hunte*, Juergen Koepke, Christian
More informationPeptides And Proteins
Kevin Burgess, May 3, 2017 1 Peptides And Proteins from chapter(s) in the recommended text A. Introduction B. omenclature And Conventions by amide bonds. on the left, right. 2 -terminal C-terminal triglycine
More informationSecondary Structure. Bioch/BIMS 503 Lecture 2. Structure and Function of Proteins. Further Reading. Φ, Ψ angles alone determine protein structure
Bioch/BIMS 503 Lecture 2 Structure and Function of Proteins August 28, 2008 Robert Nakamoto rkn3c@virginia.edu 2-0279 Secondary Structure Φ Ψ angles determine protein structure Φ Ψ angles are restricted
More informationBiophysics 490M Project
Biophysics 490M Project Dan Han Department of Biochemistry Structure Exploration of aa 3 -type Cytochrome c Oxidase from Rhodobacter sphaeroides I. Introduction: All organisms need energy to live. They
More informationPhysiochemical Properties of Residues
Physiochemical Properties of Residues Various Sources C N Cα R Slide 1 Conformational Propensities Conformational Propensity is the frequency in which a residue adopts a given conformation (in a polypeptide)
More informationLagrange Multipliers
Optimization with Constraints As long as algebra and geometry have been separated, their progress have been slow and their uses limited; but when these two sciences have been united, they have lent each
More informationBahnson 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
More informationSupporting Information
Supporting Information Micelle-Triggered b-hairpin to a-helix Transition in a 14-Residue Peptide from a Choline-Binding Repeat of the Pneumococcal Autolysin LytA HØctor Zamora-Carreras, [a] Beatriz Maestro,
More informationStructural 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
More informationExam 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
More informationOxygen Binding in Hemocyanin
Supporting Information for Quantum Mechanics/Molecular Mechanics Study of Oxygen Binding in Hemocyanin Toru Saito and Walter Thiel* Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470
More informationSUPPLEMENTARY 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
More informationPacking of Secondary Structures
7.88 Lecture Notes - 4 7.24/7.88J/5.48J The Protein Folding and Human Disease Professor Gossard Retrieving, Viewing Protein Structures from the Protein Data Base Helix helix packing Packing of Secondary
More informationDetailed description of overall and active site architecture of PPDC- 3dThDP, PPDC-2HE3dThDP, PPDC-3dThDP-PPA and PPDC- 3dThDP-POVA
Online Supplemental Results Detailed description of overall and active site architecture of PPDC- 3dThDP, PPDC-2HE3dThDP, PPDC-3dThDP-PPA and PPDC- 3dThDP-POVA Structure solution and overall architecture
More informationProblem Set 1
2006 7.012 Problem Set 1 Due before 5 PM on FRIDAY, September 15, 2006. Turn answers in to the box outside of 68-120. PLEASE WRITE YOUR ANSWERS ON THIS PRINTOUT. 1. For each of the following parts, pick
More informationSteered Molecular Dynamics Simulation of the Rieske Subunit Motion in the Cytochrome bc 1 Complex
Biophysical Journal Volume 77 October 1999 1753 1768 1753 Steered Molecular Dynamics Simulation of the Rieske Subunit Motion in the Cytochrome bc 1 Complex Sergei Izrailev,* # Antony R. Crofts, Edward
More informationCHMI 2227 EL. Biochemistry I. Test January Prof : Eric R. Gauthier, Ph.D.
CHMI 2227 EL Biochemistry I Test 1 26 January 2007 Prof : Eric R. Gauthier, Ph.D. Guidelines: 1) Duration: 55 min 2) 14 questions, on 7 pages. For 70 marks (5 marks per question). Worth 15 % of the final
More informationSupporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1
Supporting information to: Time-resolved observation of protein allosteric communication Sebastian Buchenberg, Florian Sittel and Gerhard Stock Biomolecular Dynamics, Institute of Physics, Albert Ludwigs
More informationIntroduction to Comparative Protein Modeling. Chapter 4 Part I
Introduction to Comparative Protein Modeling Chapter 4 Part I 1 Information on Proteins Each modeling study depends on the quality of the known experimental data. Basis of the model Search in the literature
More informationSupporting information
Electronic Supplementary Material (ESI) for New Journal of Chemistry. This journal is The Royal Society of Chemistry and the Centre National de la Recherche Scientifique 2015 Supporting information Influence
More informationMajor Types of Association of Proteins with Cell Membranes. From Alberts et al
Major Types of Association of Proteins with Cell Membranes From Alberts et al Proteins Are Polymers of Amino Acids Peptide Bond Formation Amino Acid central carbon atom to which are attached amino group
More informationSupplementary 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,
More informationSUPPLEMENTARY 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,
More information6 Discussion. 6.1 Bacterial reaction center X-Ray crystallography of RC mutants
6.1 Bacterial reaction center Proton and electron transfer in bacterial reaction centers were investigated using time-resolved FTIR spectroscopy and X-ray crystallography. The effect of sitespecific mutations
More informationCentral Dogma. modifications genome transcriptome proteome
entral Dogma DA ma protein post-translational modifications genome transcriptome proteome 83 ierarchy of Protein Structure 20 Amino Acids There are 20 n possible sequences for a protein of n residues!
More informationSUPPLEMENTARY 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
More informationBacterial 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,
More informationSupplementary 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,
More informationWhat 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
More informationSupporting Online Material for
www.sciencemag.org/cgi/content/full/310/5751/1159/dc1 Supporting Online Material for Structure of the Quaternary Complex of Interleukin-2 with Its α, β, and γ c Receptors Xinquan Wang, Mathias Rickert,
More informationAmino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate
Amino Acid Side Chain Induced Selectivity in the Hydrolysis of Peptides Catalyzed by a Zr(IV)-Substituted Wells-Dawson Type Polyoxometalate Stef Vanhaecht, Gregory Absillis, Tatjana N. Parac-Vogt* Department
More informationUnraveling the degradation of artificial amide bonds in Nylon oligomer hydrolase: From induced-fit to acylation processes
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2015 Supporting Information for Unraveling the degradation of artificial amide bonds
More informationClustering and Model Integration under the Wasserstein Metric. Jia Li Department of Statistics Penn State University
Clustering and Model Integration under the Wasserstein Metric Jia Li Department of Statistics Penn State University Clustering Data represented by vectors or pairwise distances. Methods Top- down approaches
More informationStructural Alignment of Proteins
Goal Align protein structures Structural Alignment of Proteins 1 2 3 4 5 6 7 8 9 10 11 12 13 14 PHE ASP ILE CYS ARG LEU PRO GLY SER ALA GLU ALA VAL CYS PHE ASN VAL CYS ARG THR PRO --- --- --- GLU ALA ILE
More informationSupplemental Materials for. Structural Diversity of Protein Segments Follows a Power-law Distribution
Supplemental Materials for Structural Diversity of Protein Segments Follows a Power-law Distribution Yoshito SAWADA and Shinya HONDA* National Institute of Advanced Industrial Science and Technology (AIST),
More informationProgramme 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
More informationTable 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
More informationSUPPLEMENTARY 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
More informationChapter 4: Amino Acids
Chapter 4: Amino Acids All peptides and polypeptides are polymers of alpha-amino acids. lipid polysaccharide enzyme 1940s 1980s. Lipids membrane 1960s. Polysaccharide Are energy metabolites and many of
More informationWhat binds to Hb in addition to O 2?
Reading: Ch5; 158-169, 162-166, 169-174 Problems: Ch5 (text); 3,7,8,10 Ch5 (study guide-facts); 1,2,3,4,5,8 Ch5 (study guide-apply); 2,3 Remember Today at 5:30 in CAS-522 is the second chance for the MB
More informationLinear Algebra. Chapter 8: Eigenvalues: Further Applications and Computations Section 8.2. Applications to Geometry Proofs of Theorems.
Linear Algebra Chapter 8: Eigenvalues: Further Applications and Computations Section 8.2. Applications to Geometry Proofs of Theorems May 1, 2018 () Linear Algebra May 1, 2018 1 / 8 Table of contents 1
More informationFinal Chem 4511/6501 Spring 2011 May 5, 2011 b Name
Key 1) [10 points] In RNA, G commonly forms a wobble pair with U. a) Draw a G-U wobble base pair, include riboses and 5 phosphates. b) Label the major groove and the minor groove. c) Label the atoms of
More informationLOWELL WEEKLY JOURNAL
Y -» $ 5 Y 7 Y Y -Y- Q x Q» 75»»/ q } # ]»\ - - $ { Q» / X x»»- 3 q $ 9 ) Y q - 5 5 3 3 3 7 Q q - - Q _»»/Q Y - 9 - - - )- [ X 7» -» - )»? / /? Q Y»» # X Q» - -?» Q ) Q \ Q - - - 3? 7» -? #»»» 7 - / Q
More informationChemistry Chapter 22
hemistry 2100 hapter 22 Proteins Proteins serve many functions, including the following. 1. Structure: ollagen and keratin are the chief constituents of skin, bone, hair, and nails. 2. atalysts: Virtually
More informationProteins: Characteristics and Properties of Amino Acids
SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.
More informationProtein Structure Bioinformatics Introduction
1 Swiss Institute of Bioinformatics Protein Structure Bioinformatics Introduction Basel, 27. September 2004 Torsten Schwede Biozentrum - Universität Basel Swiss Institute of Bioinformatics Klingelbergstr
More informationBiological Macromolecules
Introduction for Chem 493 Chemistry of Biological Macromolecules Dr. L. Luyt January 2008 Dr. L. Luyt Chem 493-2008 1 Biological macromolecules are the molecules of life allow for organization serve a
More informationRamachandran Plot. 4ysz Phi (degrees) Plot statistics
B Ramachandran Plot ~b b 135 b ~b ~l l Psi (degrees) 5-5 a A ~a L - -135 SER HIS (F) 59 (G) SER (B) ~b b LYS ASP ASP 315 13 13 (A) (F) (B) LYS ALA ALA 315 173 (E) 173 (E)(A) ~p p ~b - -135 - -5 5 135 (degrees)
More informationProtein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version Document Published by the wwpdb
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.30 Document Published by the wwpdb This format complies with the PDB Exchange Dictionary (PDBx) http://mmcif.pdb.org/dictionaries/mmcif_pdbx.dic/index/index.html.
More informationBiomolecules: lecture 10
Biomolecules: lecture 10 - understanding in detail how protein 3D structures form - realize that protein molecules are not static wire models but instead dynamic, where in principle every atom moves (yet
More informationAny 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
More informationfrom Pseudomonas stutzeri determined at 2.2 Å resolution Anders Kadziola and Sine Larsen*
Research Article 203 Crystal structure of the dihaem cytochrome c 4 from Pseudomonas stutzeri determined at 2.2 Å resolution Anders Kadziola and Sine Larsen* Background: Cytochromes c 4 are dihaem cytochromes
More informationSUPPLEMENTARY INFORMATION
Table of Contents Page Supplementary Table 1. Diffraction data collection statistics 2 Supplementary Table 2. Crystallographic refinement statistics 3 Supplementary Fig. 1. casic1mfc packing in the R3
More information12. Stresses and Strains
12. Stresses and Strains Finite Element Method Differential Equation Weak Formulation Approximating Functions Weighted Residuals FEM - Formulation Classification of Problems Scalar Vector 1-D T(x) u(x)
More informationViewing 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
More informationApplications of Eigenvalues & Eigenvectors
Applications of Eigenvalues & Eigenvectors Louie L. Yaw Walla Walla University Engineering Department For Linear Algebra Class November 17, 214 Outline 1 The eigenvalue/eigenvector problem 2 Principal
More informationsite in the original data set (1PRC) was reexamined using the structure of the UQ9-depleted RC as a reference. A modified Q B
Research Article 1339 The coupling of light-induced electron transfer and proton uptake as derived from crystal structures of reaction centres from Rhodopseudomonas viridis modified at the binding site
More information7.012 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
More informationIntroduction 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
More informationDetails of Protein Structure
Details of Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Anne Mølgaard, Kemisk Institut, Københavns Universitet Learning Objectives
More informationOther 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
More informationPotassium channel gating and structure!
Reading: Potassium channel gating and structure Hille (3rd ed.) chapts 10, 13, 17 Doyle et al. The Structure of the Potassium Channel: Molecular Basis of K1 Conduction and Selectivity. Science 280:70-77
More informationml. ph 7.5 ph 6.5 ph 5.5 ph 4.5. β 2 AR-Gs complex + GDP β 2 AR-Gs complex + GTPγS
a UV28 absorption (mau) 9 8 7 5 3 β 2 AR-Gs complex β 2 AR-Gs complex + GDP β 2 AR-Gs complex + GTPγS β 2 AR-Gs complex dissociated complex excess nucleotides b 9 8 7 5 3 β 2 AR-Gs complex β 2 AR-Gs complex
More informationSUPPLEMENTARY 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
More informationCHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis
CHEM 463: Advanced Inorganic Chemistry Modeling Metalloproteins for Structural Analysis Purpose: The purpose of this laboratory is to introduce some of the basic visualization and modeling tools for viewing
More informationENZYME MECHANISMS, PROTEASES, STRUCTURAL BIOLOGY
Supplementary Information SUBJECT AREAS: ENZYME MECHANISMS, PROTEASES, STRUCTURAL BIOLOGY Correspondence and requests for materials should be addressed to N.T. (ntanaka@pharm.showa-u.ac.jp) or W.O. (owataru@vos.nagaokaut.ac.jp)
More informationHSQC spectra for three proteins
HSQC spectra for three proteins SH3 domain from Abp1p Kinase domain from EphB2 apo Calmodulin What do the spectra tell you about the three proteins? HSQC spectra for three proteins Small protein Big protein
More informationSUPPLEMENTARY 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
More informationSolutions In each case, the chirality center has the R configuration
CAPTER 25 669 Solutions 25.1. In each case, the chirality center has the R configuration. C C 2 2 C 3 C(C 3 ) 2 D-Alanine D-Valine 25.2. 2 2 S 2 d) 2 25.3. Pro,, Trp, Tyr, and is, Trp, Tyr, and is Arg,
More informationPotential Energy (hyper)surface
The Molecular Dynamics Method Thermal motion of a lipid bilayer Water permeation through channels Selective sugar transport Potential Energy (hyper)surface What is Force? Energy U(x) F = " d dx U(x) Conformation
More informationIon Translocation Across Biological Membranes. Janos K. Lanyi University of California, Irvine
Ion Translocation Across Biological Membranes Janos K. Lanyi University of California, Irvine Examples of transmembrane ion pumps Protein Cofactor, substrate, etc. MW Subunits Mitoch. cytochrome oxidase
More informationCrystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas viridis
J. MoL BioL (1995) 246, 429-457 JMB O Crystallographic Refinement at 2.3 A Resolution and Refined Model of the Photosynthetic Reaction Centre from Rhodopseudomonas viridis Johann Deisenhofer, Otto Epp,
More informationSI 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.
More informationNMR 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
More informationSUPPLEMENTARY 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
More informationC H E M I S T R Y N A T I O N A L Q U A L I F Y I N G E X A M I N A T I O N SOLUTIONS GUIDE
C H E M I S T R Y 2 0 0 0 A T I A L Q U A L I F Y I G E X A M I A T I SLUTIS GUIDE Answers are a guide only and do not represent a preferred method of solving problems. Section A 1B, 2A, 3C, 4C, 5D, 6D,
More informationProtein Structure and Visualisation. Introduction to PDB and PyMOL
Protein Structure and Visualisation Introduction to PDB and PyMOL 1 Feedback Persons http://www.bio-evaluering.dk/ 2 Program 8.00-8.15 Quiz results 8.15-8.50 Introduction to PDB & PyMOL 8.50-9.00 Break
More informationRanjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India. 1 st November, 2013
Hydration of protein-rna recognition sites Ranjit P. Bahadur Assistant Professor Department of Biotechnology Indian Institute of Technology Kharagpur, India 1 st November, 2013 Central Dogma of life DNA
More informationSupplementary 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
More informationFull 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,
More informationSupplemental 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
More informationElectronic Supplementary Information
Electronic Supplementary Information A Sensitive Phosphorescent Thiol Chemosensor Based on an Iridium(III) Complex with α,β-unsaturated Ketone Functionalized 2,2 -Bipyridyl Ligand Na Zhao, a Yu-Hui Wu,
More informationNeatest and Promptest Manner. E d i t u r ami rul)lihher. FOIt THE CIIILDIIES'. Trifles.
» ~ $ ) 7 x X ) / ( 8 2 X 39 ««x» ««! «! / x? \» «({? «» q «(? (?? x! «? 8? ( z x x q? ) «q q q ) x z x 69 7( X X ( 3»«! ( ~«x ««x ) (» «8 4 X «4 «4 «8 X «x «(» X) ()»» «X «97 X X X 4 ( 86) x) ( ) z z
More informationSupporting 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
More informationProtein structures and comparisons ndrew Torda Bioinformatik, Mai 2008
Protein structures and comparisons ndrew Torda 67.937 Bioinformatik, Mai 2008 Ultimate aim how to find out the most about a protein what you can get from sequence and structure information On the way..
More informationATPase Synthase - A Molecular Double Motor
ATPase Synthase - A Molecular Double Motor RC bc 1 bc 1 ATPase Photosynthesic Unit of Purple Bacteria Module that converts sun light into chemical energy (ATP) Light in hν H + Q/QH 2 /Q bc 1 ADP ATP out
More informationApril, The energy functions include:
REDUX A collection of Python scripts for torsion angle Monte Carlo protein molecular simulations and analysis The program is based on unified residue peptide model and is designed for more efficient exploration
More informationExam III. Please read through each question carefully, and make sure you provide all of the requested information.
09-107 onors Chemistry ame Exam III Please read through each question carefully, and make sure you provide all of the requested information. 1. A series of octahedral metal compounds are made from 1 mol
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature12045 Supplementary Table 1 Data collection and refinement statistics. Native Pt-SAD X-ray source SSRF BL17U SPring-8 BL41XU Wavelength (Å) 0.97947 1.07171 Space group P2 1 2 1 2 1 P2
More informationData File Formats. There are dozens of file formats for chemical data.
1 Introduction There are dozens of file formats for chemical data. We will do an overview of a few that are often used in structural bioinformatics. 2 1 PDB File Format (1) The PDB file format specification
More informationNature Structural and Molecular Biology: doi: /nsmb.2938
Supplementary Figure 1 Characterization of designed leucine-rich-repeat proteins. (a) Water-mediate hydrogen-bond network is frequently visible in the convex region of LRR crystal structures. Examples
More informationHomework 1/Solutions. Graded Exercises
MTH 310-3 Abstract Algebra I and Number Theory S18 Homework 1/Solutions Graded Exercises Exercise 1. Below are parts of the addition table and parts of the multiplication table of a ring. Complete both
More information