Molecular Graphics with PyMOL
|
|
|
- Sharleen Ross
- 5 years ago
- Views:
Transcription
1 Molecular Graphics with PyMOL Jean)YvesSgro Instructors Molecular Graphics & Scientific Communication Ann Palmenberg Jean-Yves Sgro Marchel Hill Holly Basta H. Adam Steinberg 1
2 Lab Book : Section 1 Computer lab location: DMCComputerLab,BiochemistryBuilding(renovated1912wing) RoomB1144 Weareherenow 2
3 hdp://publicagons.nigms.nih.gov/order/! ScienceEduca:onBooklets Free NIH publications insidethecell.pdf structlife.pdf medbydesign.pdf coh.pdf FindingsMagazine compugng_life.pdf hdp://publicagons.nigms.nih.gov/order/ 3
4 History: the beginnings Experimental methods that generate 3D data Protein Data Bank Coordinates PyMOL interface Overview of: molecular graphics beginnings bycyruslevinthal hdp:// 4
5 Endeavour Volume 26, Issue 4, 1 December 2002, Pages hdp:// hdps:// 5
6 Endeavour Volume 26, Issue 4, 1 December 2002, Pages hdp:// hdps:// Evans&Sutherland, :45 min! 6
7 TomatoBushyStuntVirusEArtOlsonE1981E hdp://molecularmovies.com/movies/olson_tbsv.mov Fulllengthmovie:7:49min DNA & RNA structure! major! groove! minor! groove! major! groove! minor! groove! 25.6 Å! 34 Å! 19 Å! 10 bp/turn! DNA: Bform 23 Å! 11 bp/turn! RNA:! A form! 19 Å! 23 Å! 7
8 Pep:debondscondense AAsintopolypep:des H! R O! +! 1! H--N--C--C! R 2! O! H! H! N--C--C! R 3! O! H! H! N--C--C! R 4! O! H! H! N--C--C! -! H! H! O! --! --! --! --! --! --! --! --! --! --! --! --! --! Structure'of'Proteins Packing,DomainsandFolds Primary Structure:!! Amino acid sequence! Ala-Glu-Val-Thr-Asp-Pro-Gly! Secondary Structure:! α helix! β sheet! turns! 1hgu Ter:aryStructure: Associa:onofsecondary structureelementsofasingle polypep:dechainintoa3d structure. Quaternary Structure: Associa:onof2'or'more polypep:dechainsforsome proteins. 1eru 1air 8
9 alpha%mo(f:%helix)turn)helix 1)calcium)bindingmuscle proteinparvalbumin(109aa)contains thehelix)loop)helixmogf3gmes.2out of3itisacalciumbindingsite.eandf arethehelixnamethatformtheef) hand: 2- DNA-binding!(procaryotes)! -cro binding protein! - lambda repressor!!dna sequence is palendromic! E! E! F! F! EF-hand! Ca++! calmodulin and troponin-c, also! Ca+ binding have the same motif! lambda repressor! SödingandLupas(2003) notedthatstructural homologyissubstangally moreconservedthrough evolugonthanis sequencehomology. Theyarguethatmodern proteinsevolvedby fusionofsimpler"building block"proteins SödingandLupasBioessays. 2003Sep;25(9):837)46 9
10 Experimental Methods 3Main: X)raycrystallography NMR Cryoelectronmicroscopy Experimental Methods Poetic The Crystal-Clear Cell Simon Bushell 9 September
11 X)raysource Bragg s law constructive destructive Accordingtothe2θdevia:on,thephaseshifcausesconstruc:veordestruc:veinterferences. hdps://en.wikipedia.org/wiki/bragg%27s_law 11
12 NOVA:SecretsofPhoto51(RosalindFranklin) hdp:// Anatomy of Photo 51 hdp:// )Franklin)s)X)ray)diffracGon) explanagon)of)x)ray)padern).html hdp:// body/dna)photograph.html 12
13 1:30min excerpt ClaudeSauter,Strasbourg FrancehDp://vimeo.com/ Electron Density Map (before) Buildphysicalmodel CouldthesearchforulGmatetruthreallyhave revealedsohideousandviscerallookingan object? )MaxPerutz(1914)2002) TheHemoglobinMolecule,Scien(fic%American,211,65)76,November
14 Sir John Kendrew with his model of myoglobin in Photograph by Max Perutz. Electron Density Map (now) Amino)acidsarebuilt withinmapcontours. hdp:// hdp://en.wikipedia.org/wiki/coot_(program) 14
15 Stanford Linear Accelerator Center (SLAC) Fullmovie(5:27min):hDp:// 27sec The%spinning%of%a% charged%object% induces%a%magne(c% field. 15
16 hdp:// hdp:// 16
17 Electrontomography PrinciplesofdataacquisiGonandreconstrucGoninECT.(A)Asetof2)DprojecGonimagesis recordedwhileglgngtheobjectaroundoneaxis.(b)theback)projecgonmethodof3)d reconstrucgoninect:foreachprojecgon,aback)projecgonbodyiscalculated,andthesum ofalltheback)projecgonbodiesrepresentsthedensitydistribugonoftheoriginalobject. Reprinted,withpermissionfrom(Baumeisteretal.1999). Tocheva et al. Electron Cryotomography. Cold Spring Harb Perspect Biol June; 2(6): a Baumeister et al. Electron tomography of molecules and cells. Trends Cell Biol Feb;9(2):81-5. Slide by Janos Hajdu, Uppsala universitet 17
18 From: Helen R. Saibil. Macromolecular structure determination by cryo-electron microscopy (October 2000) Biological Crystallography 56(10): :2structures 1974:12proteinstructures. Tuesday Oct 30, 2012 :85,848 structures. 18
19 1971:2structures 1974:12proteinstructures. Thursday Nov 7, 2013 :95,280 structures. As of Tuesday Oct 30, 2012 at 5 PM PDT Exp.Method Proteins Nucleic Acids Protein/NA Complexes Other Total Total % X-RAY % NMR % ELECTRON MICROSCOP Y % HYBRID % other % Total % X)RAY NMR ELECTRONMICROSCOPY HYBRID other 19
20 Plain Text 80 columns! ! Header 3D coordinates Connectivity End records HEADER CALCIUM-BINDING PROTEIN 08-OCT-93 1CDM 1CDM 2 COMPND CALMODULIN COMPLEXED WITH CALMODULIN-BINDING DOMAIN OF 1CDM 3 COMPND 2 CALMODULIN-DEPENDENT PROTEIN KINASE II 1CDM 4 SOURCE CALMODULIN: BOVINE (BOS TAURUS) BRAIN; PEPTIDE: SYNTHETIC 1CDM 5 SOURCE 2 BASED ON BOVINE (BOS TAURUS) BRAIN CALMODULIN-BINDING 1CDM 6 SOURCE 3 DOMAIN OF CALMODULIN-DEPENDENT PROTEIN KINASE 1CDM 7 AUTHOR W.E.MEADOR,F.A.QUIOCHO 1CDM 8 REVDAT 1 31-AUG-94 1CDM 0 1CDM 9 JRNL AUTH W.E.MEADOR,A.R.MEANS,F.A.QUIOCHO 1CDM 10 JRNL TITL MODULATION OF CALMODULIN PLASTICITY IN MOLECULAR 1CDM 11 JRNL TITL 2 RECOGNITION ON THE BASIS OF X-RAY STRUCTURES 1CDM 12 JRNL REF SCIENCE V CDM 13 JRNL REFN ASTM SCIEAS US ISSN CDM 14 // SEQRES 1 A 144 LEU THR GLU GLU GLN ILE ALA GLU PHE LYS GLU ALA PHE 1CDM 52 SEQRES 2 A 144 SER LEU PHE ASP LYS ASP GLY ASP GLY THR ILE THR THR 1CDM 53 SEQRES 3 A 144 LYS GLU LEU GLY THR VAL MET ARG SER LEU GLY GLN ASN 1CDM 54 // SEQRES 1 B 25 LEU LYS LYS PHE ASN ALA ARG ARG LYS LEU LYS GLY ALA 1CDM 64 SEQRES 2 B 25 ILE LEU THR THR MET LEU ALA THR ARG ASN PHE SER 1CDM 65 HET CA A 1 1 CALCIUM +2 COUNTER ION 1CDM 66 HET CA A 2 1 CALCIUM +2 COUNTER ION 1CDM 67 HET CA A 3 1 CALCIUM +2 COUNTER ION 1CDM 68 HET CA A 4 1 CALCIUM +2 COUNTER ION 1CDM 69 FORMUL 3 CA 4(CA1 ++) 1CDM 70 FORMUL 4 HOH *53(H2 O1) 1CDM 71 CRYST C CDM 72 ORIGX CDM 73 ORIGX CDM 74 ORIGX CDM 75 SCALE CDM 76 SCALE CDM 77 SCALE CDM 78 20
21 ATOM Serial # Atom Type Amino Acid Chain ID Sequence # X Y Z coordinates Occupancy (Scale Factor) Temperature Factor ATOM 1 N LEU A CDM 79 ATOM 2 CA LEU A CDM 80 ATOM 3 C LEU A CDM 81 ATOM 4 O LEU A CDM 82 ATOM 5 CB LEU A CDM 83 ATOM 6 CG LEU A CDM 84 ATOM 7 CD1 LEU A CDM 85 ATOM 8 CD2 LEU A CDM 86 ATOM 9 N THR A CDM 87 ATOM 10 CA THR A CDM 88 // ATOM 1037 O THR A CDM1115 ATOM 1038 CB THR A CDM1116 ATOM 1039 OG1 THR A CDM1117 ATOM 1040 CG2 THR A CDM1118 HETATM 1041 CA CA A CDM1119 HETATM 1042 CA CA A CDM1120 HETATM 1043 CA CA A CDM1121 HETATM 1044 CA CA A CDM1122 ATOM 1045 N PHE B CDM1123 ATOM 1046 CA PHE B CDM1124 ATOM 1047 C PHE B CDM1125 ATOM 1048 O PHE B CDM1126 ATOM 1049 CB PHE B CDM1127 ATOM 1050 CG PHE B CDM1128 ATOM 1051 CD1 PHE B CDM1129 ATOM 1052 CD2 PHE B CDM1130 ATOM 1053 CE1 PHE B CDM1131 // Optional hdp://en.wikipedia.org/wiki/cartesian_coordinate_system The idea of this system was developed in 1637 in two writings by Descartes and independently by Pierre de Fermat, although Fermat used three dimensions and did not publish the discovery. (Ref: "analytic geometry". Encyclopædia Britannica (Encyclopædia Britannica Online ed.) )! 21
22 René Descartes (CartesiusinLaGn). ATOM 1181 CB THR B CDM1259 ATOM 1182 OG1 THR B CDM1260 ATOM 1183 CG2 THR B CDM1261 TER 1184 THR B 310 1CDM1262 HETATM 1185 O HOH CDM1263 HETATM 1186 O HOH CDM1264 HETATM 1187 O HOH CDM1265 // HETATM 1235 O HOH CDM1313 HETATM 1236 O HOH CDM1314 HETATM 1237 O HOH CDM1315 CONECT CDM1316 CONECT CDM1317 // CONECT CDM1330 CONECT CDM1331 CONECT CDM1332 CONECT CDM1333 CONECT CDM1334 MASTER CDM1335 END 22
23 Record Type MODEL&ENDMDL! X Y Z coordinates MODEL 1! ATOM 1 O5' G A O! ATOM 2 C5' G A C! //! ATOM 768 H6 C A H! TER 769 C A 24! ENDMDL! MODEL 2! ATOM 1 O5' G A O! ATOM 2 C5' G A C / / ENDMDL! MODEL 3! ATOM 1 O5' G A O! ATOM 2 C5' G A C / / ! MODEL 1 ATOM LINES FOR CHAIN A TER ATOM LINES FOR CHAIN B TER ENDMDL MODEL 2 ATOM LINES FOR CHAIN A TER ATOM LINES FOR CHAIN B TER ENDMDL Header 3D coordinates MODEL 1 3D coordinates MODEL 2 Connectivity End records 23
24 Example 1: 2biw APOCAROTENOIDCLEAVAGEOXYGENASE Biological Unit 1 + Biological Unit 2 Asymmetric Unit Biological Unit 3 + Biological Unit 4 Example 2: 1DUD Escherichia coli dutpase in complex with a substrate analogue (dudp). Asymmetric Unit x 3 = Assumed Biological Molecules REMARK 350 BIOMOLECULE: 1! REMARK 350 APPLY THE FOLLOWING TO CHAINS: A! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! REMARK 350 BIOMT ! 24
25 Example 3: 1AYM HUMANRHINOVIRUS16COATPROTEINATHIGHRESOLUTION Asymmetric Unit x 60 = Assumed Biological Molecules MOLECULE Py MOL 25
26 Upper Control Window Movie Controls 26
27 Upper Control Window Movie Controls 27
28 Action Show Hide Label Color) Middle Right Lef 28
29 Lef 29
30 Export Movie Store Recall Create Movie Settings Example F1-F5 F1)2)3)4)5/4sec/Y)Rock/14.8Mb/MPEG 30
31 31
X-ray crystallography NMR Cryoelectron microscopy
Molecular Graphics with PyMOL Overview of: Protein Data Bank Coordinates Jean-Yves Sgro PyMOL interface Hands-on! Experimental Methods 3 Main: X-ray crystallography NMR Cryoelectron microscopy X-ray source
Details 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
Protein 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
Working with protein structures. Benjamin Jack
Working with protein structures Benjamin Jack Structure of Triosephosphate Isomerase PDB ID: 1HTI loop beta sheet alpha helix Different perspectives of the same structure Structure of Truncated Hemoglobin
Protein 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.
Data 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
Protein Structure Determination. Why Bother With Structure? Protein Sequences Far Outnumber Structures. Growth of Structural Data
Protein Structure Determination Why Bother With Structure? The amino acid sequence of a protein contains interesting information. A protein sequence can be compared to other protein sequences to establish
Proteins. Central Dogma : DNA RNA protein Amino acid polymers - defined composition & order. Perform nearly all cellular functions Drug Targets
Proteins Central Dogma : DNA RNA protein Amino acid polymers - defined composition & order Perform nearly all cellular functions Drug Targets Fold into discrete shapes. Proteins - cont. Specific shapes
Chapter 2 Structures. 2.1 Introduction Storing Protein Structures The PDB File Format
Chapter 2 Structures 2.1 Introduction The three-dimensional (3D) structure of a protein contains a lot of information on its function, and can be used for devising ways of modifying it (propose mutants,
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
HIV protease inhibitor. Certain level of function can be found without structure. But a structure is a key to understand the detailed mechanism.
Proteins are linear polypeptide chains (one or more) Building blocks: 20 types of amino acids. Range from a few 10s-1000s They fold into varying three-dimensional shapes structure medicine Certain level
Drug targets, Protein Structures and Crystallography
Drug targets, Protein Structures and Crystallography NS5B viral RNA polymerase (RNA dep) Hepa88s C drug Sofosbuvir (Sovaldi) FDA 2013 Epclusa - combina8on with Velpatasvir approved in in 2016) Prodrug
Protein Structure Determination. Why Bother With Structure? Protein Sequences Far Outnumber Structures
Protein Structure Determination How are these structures determined? Why Bother With Structure? The amino acid sequence of a protein contains interesting information. A protein sequence can be compared
Protein Structure Determination. How are these structures determined?
Protein Structure Determination How are these structures determined? Why Bother With Structure? The amino acid sequence of a protein contains interesting information. A protein sequence can be compared
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
Ranjit 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
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
Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination
Lecture 9 M230 Feigon Sequential resonance assignments in (small) proteins: homonuclear method 2º structure determination Reading resources v Roberts NMR of Macromolecules, Chap 4 by Christina Redfield
Bioinformatics. Macromolecular structure
Bioinformatics Macromolecular structure Contents Determination of protein structure Structure databases Secondary structure elements (SSE) Tertiary structure Structure analysis Structure alignment Domain
Amino 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
Secondary 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
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.
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,
Central 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!
Physiochemical 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)
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description. Version 3.0, December 1, 2006 Updated to Version 3.
Protein Data Bank Contents Guide: Atomic Coordinate Entry Format Description Version 3.0, December 1, 2006 Updated to Version 3.01 March 30, 2007 1. Introduction The Protein Data Bank (PDB) is an archive
Protein Structures: Experiments and Modeling. Patrice Koehl
Protein Structures: Experiments and Modeling Patrice Koehl Structural Bioinformatics: Proteins Proteins: Sources of Structure Information Proteins: Homology Modeling Proteins: Ab initio prediction Proteins:
Introduction to" Protein Structure
Introduction to" Protein Structure Function, evolution & experimental methods Thomas Blicher, Center for Biological Sequence Analysis Learning Objectives Outline the basic levels of protein structure.
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
Proteins: Characteristics and Properties of Amino Acids
SBI4U:Biochemistry Macromolecules Eachaminoacidhasatleastoneamineandoneacidfunctionalgroupasthe nameimplies.thedifferentpropertiesresultfromvariationsinthestructuresof differentrgroups.thergroupisoftenreferredtoastheaminoacidsidechain.
Properties of amino acids in proteins
Properties of amino acids in proteins one of the primary roles of DNA (but not the only one!) is to code for proteins A typical bacterium builds thousands types of proteins, all from ~20 amino acids repeated
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)
Packing 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
Advanced Topics in RNA and DNA. DNA Microarrays Aptamers
Quiz 1 Advanced Topics in RNA and DNA DNA Microarrays Aptamers 2 Quantifying mrna levels to asses protein expression 3 The DNA Microarray Experiment 4 Application of DNA Microarrays 5 Some applications
Supporting 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
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
Protein Structure: Data Bases and Classification Ingo Ruczinski
Protein Structure: Data Bases and Classification Ingo Ruczinski Department of Biostatistics, Johns Hopkins University Reference Bourne and Weissig Structural Bioinformatics Wiley, 2003 More References
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
Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information
Amino Acids and Proteins at ZnO-water Interfaces in Molecular Dynamics Simulations: Electronic Supplementary Information Grzegorz Nawrocki and Marek Cieplak Institute of Physics, Polish Academy of Sciences,
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
Biological 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
Supersecondary Structures (structural motifs)
Supersecondary Structures (structural motifs) Various Sources Slide 1 Supersecondary Structures (Motifs) Supersecondary Structures (Motifs): : Combinations of secondary structures in specific geometric
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 06:13 pm GMT PDB ID : 5G5C Title : Structure of the Pyrococcus furiosus Esterase Pf2001 with space group C2221 Authors : Varejao, N.; Reverter,
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Feb 17, 2018 01:16 am GMT PDB ID : 1IFT Title : RICIN A-CHAIN (RECOMBINANT) Authors : Weston, S.A.; Tucker, A.D.; Thatcher, D.R.; Derbyshire, D.J.; Pauptit,
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
Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013
Protein Structure Marianne Øksnes Dalheim, PhD candidate Biopolymers, TBT4135, Autumn 2013 The presentation is based on the presentation by Professor Alexander Dikiy, which is given in the course compedium:
April, 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
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
Figure 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
BIOINF 4120 Bioinformatics 2 - Structures and Systems -
BIOINF 4120 Bioinformatics 2 - Structures and Systems - Oliver Kohlbacher Summer 2014 5. Structure Elucidation Overview Protein structure elucidation X-ray diffraction (XRD) Crystallization Physics of
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,
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
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Jan 14, 2019 11:10 AM EST PDB ID : 6GYW Title : Crystal structure of DacA from Staphylococcus aureus Authors : Tosi, T.; Freemont, P.S.; Grundling, A. Deposited
3D Visualization of Drugs-Protein Complexes
3D Visualization of Drugs-Protein Complexes Goal: Develop better understanding of Protein Database and its entries Plan Introductory information about protein structure database Learn Molsoft-browser for
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,
BIRKBECK COLLEGE (University of London)
BIRKBECK COLLEGE (University of London) SCHOOL OF BIOLOGICAL SCIENCES M.Sc. EXAMINATION FOR INTERNAL STUDENTS ON: Postgraduate Certificate in Principles of Protein Structure MSc Structural Molecular Biology
Peptides 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
C CH 3 N C COOH. Write the structural formulas of all of the dipeptides that they could form with each other.
hapter 25 Biochemistry oncept heck 25.1 Two common amino acids are 3 2 N alanine 3 2 N threonine Write the structural formulas of all of the dipeptides that they could form with each other. The carboxyl
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
Chemistry 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
Exam 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
PROTEIN SECONDARY STRUCTURE PREDICTION: AN APPLICATION OF CHOU-FASMAN ALGORITHM IN A HYPOTHETICAL PROTEIN OF SARS VIRUS
Int. J. LifeSc. Bt & Pharm. Res. 2012 Kaladhar, 2012 Research Paper ISSN 2250-3137 www.ijlbpr.com Vol.1, Issue. 1, January 2012 2012 IJLBPR. All Rights Reserved PROTEIN SECONDARY STRUCTURE PREDICTION:
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
Protein Fragment Search Program ver Overview: Contents:
Protein Fragment Search Program ver 1.1.1 Developed by: BioPhysics Laboratory, Faculty of Life and Environmental Science, Shimane University 1060 Nishikawatsu-cho, Matsue-shi, Shimane, 690-8504, Japan
Introduction 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
Introduction to Polymer Physics
Introduction to Polymer Physics Enrico Carlon, KU Leuven, Belgium February-May, 2016 Enrico Carlon, KU Leuven, Belgium Introduction to Polymer Physics February-May, 2016 1 / 28 Polymers in Chemistry and
Energy and Cellular Metabolism
1 Chapter 4 About This Chapter Energy and Cellular Metabolism 2 Energy in biological systems Chemical reactions Enzymes Metabolism Figure 4.1 Energy transfer in the environment Table 4.1 Properties of
NMR Assignments using NMRView II: Sequential Assignments
NMR Assignments using NMRView II: Sequential Assignments DO THE FOLLOWING, IF YOU HAVE NOT ALREADY DONE SO: For Mac OS X, you should have a subdirectory nmrview. At UGA this is /Users/bcmb8190/nmrview.
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
Read more about Pauling and more scientists at: Profiles in Science, The National Library of Medicine, profiles.nlm.nih.gov
2018 Biochemistry 110 California Institute of Technology Lecture 2: Principles of Protein Structure Linus Pauling (1901-1994) began his studies at Caltech in 1922 and was directed by Arthur Amos oyes to
Protein Structure Prediction and Display
Protein Structure Prediction and Display Goal Take primary structure (sequence) and, using rules derived from known structures, predict the secondary structure that is most likely to be adopted by each
Final 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
Clustering 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
Computational structural biology and bioinformatics
Computational structural biology and bioinformatics What is it all about? Why take it? What are we going to be doing? Organizational notes. Grades etc. Books. CS6104. Spring CS6104. 04. Spring Alexey 04.
Ramachandran 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)
Deciphering the Rules for Amino Acid Co- Assembly Based on Interlayer Distances
Supporting Information Deciphering the Rules for Amino Acid Co- Assembly Based on Interlayer Distances Santu Bera, Sudipta Mondal, Yiming Tang, Guy Jacoby, Elad Arad, ǁ Tom Guterman, Raz Jelinek, ǁ Roy
Course Notes: Topics in Computational. Structural Biology.
Course Notes: Topics in Computational Structural Biology. Bruce R. Donald June, 2010 Copyright c 2012 Contents 11 Computational Protein Design 1 11.1 Introduction.........................................
Amino Acids and Peptides
Amino Acids Amino Acids and Peptides Amino acid a compound that contains both an amino group and a carboxyl group α-amino acid an amino acid in which the amino group is on the carbon adjacent to the carboxyl
Report of protein analysis
Report of protein analysis By the WHAT IF program 2010-09-19 1 Introduction what check is the name of the validation option in what if. It doesn t matter whether you use the what check program or the what
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,
A) at equilibrium B) endergonic C) endothermic D) exergonic E) exothermic.
CHEM 2770: Elements of Biochemistry Mid Term EXAMINATION VERSION A Date: October 29, 2014 Instructor: H. Perreault Location: 172 Schultz Time: 4 or 6 pm. Duration: 1 hour Instructions Please mark the Answer
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
Peptide Syntheses. Illustrative Protection: BOC/ t Bu. A. Introduction. do not acid
Kevin Burgess, May 3, 2017 1 Peptide yntheses from chapter(s) in the recommended text A. Introduction do not acid -Met-e- -Met-Met- -e-e- -e-met- dipeptide dipeptide dipeptide dipeptide diketopiperazine
UNIT TWELVE. a, I _,o "' I I I. I I.P. l'o. H-c-c. I ~o I ~ I / H HI oh H...- I II I II 'oh. HO\HO~ I "-oh
UNT TWELVE PROTENS : PEPTDE BONDNG AND POLYPEPTDES 12 CONCEPTS Many proteins are important in biological structure-for example, the keratin of hair, collagen of skin and leather, and fibroin of silk. Other
Full wwpdb X-ray Structure Validation Report i
Full wwpdb X-ray Structure Validation Report i Mar 8, 2018 08:34 pm GMT PDB ID : 1RUT Title : Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain Authors : Deane, J.E.; Ryan, D.P.; Maher, M.J.;
PRI-Modeler: Extracting RNA structural elements from PDB files of protein RNA complexes
PRI-Modeler: Extracting RNA structural elements from PDB files of protein RNA complexes Kyungsook Han *, Chirag Nepal School of Computer Science and Engineering, Inha University, Inchon 402-751, Republic
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
X-Ray structure analysis
X-Ray structure analysis Kay Diederichs kay.diederichs@uni-konstanz.de Analysis of what? Proteins ( /ˈproʊˌtiːnz/ or /ˈproʊti.ɨnz/) are biochemical compounds consisting of one or more polypeptides typically
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...
Chapter 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
Major 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
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
Section Week 3. Junaid Malek, M.D.
Section Week 3 Junaid Malek, M.D. Biological Polymers DA 4 monomers (building blocks), limited structure (double-helix) RA 4 monomers, greater flexibility, multiple structures Proteins 20 Amino Acids,
B O C 4 H 2 O O. NOTE: The reaction proceeds with a carbonium ion stabilized on the C 1 of sugar A.
hbcse 33 rd International Page 101 hemistry lympiad Preparatory 05/02/01 Problems d. In the hydrolysis of the glycosidic bond, the glycosidic bridge oxygen goes with 4 of the sugar B. n cleavage, 18 from
Unraveling 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
Protein Struktur. Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep. wake up at slide 39
Protein Struktur Biologen und Chemiker dürfen mit Handys spielen (leise) go home, go to sleep wake up at slide 39 Andrew Torda, Wintersemester 2016/ 2017 Andrew Torda 17.10.2016 [ 1 ] Proteins - who cares?
Protein Struktur (optional, flexible)
Protein Struktur (optional, flexible) 22/10/2009 [ 1 ] Andrew Torda, Wintersemester 2009 / 2010, AST nur für Informatiker, Mathematiker,.. 26 kt, 3 ov 2009 Proteins - who cares? 22/10/2009 [ 2 ] Most important
Computational Molecular Modeling
Computational Molecular Modeling Lecture 1: Structure Models, Properties Chandrajit Bajaj Today s Outline Intro to atoms, bonds, structure, biomolecules, Geometry of Proteins, Nucleic Acids, Ribosomes,
Bioinformatics Practical for Biochemists
Bioinformatics Practical for Biochemists Andrei Lupas, Birte Höcker, Steffen Schmidt WS 2013/14 03. Sequence Features Targeting proteins signal peptide targets proteins to the secretory pathway N-terminal
Report of protein analysis
Report of protein analysis By the WHAT IF program 2010-09-19 1 Introduction what check is the name of the validation option in what if. It doesn t matter whether you use the what check program or the what