1. Online Counseling Resource YCMOU ELearning Drive… School of Architecture, Science and Technology Yashwantrao Chavan Maharashtra Open University, Nashik – 422222, India

2. OC-SBI074-CP1-01 Introduction Programmes and Courses  SEP –SBI074-CP1_U01

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari MSc (Botany), P.G. D.C. Bio-Informatics sonalisa_alkari@yahoo.com

4. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.4 How to Use This Resource  Counselor at each study center should use this presentation to deliver lecture of 40-60 minutes during Face-To-Face counseling.  Discussion about students difficulties or tutorial with assignments should follow the lecture for about 40-60 minutes.  Handouts (with 6 slides on each A4 size page) of this presentation should be provided to each student.  Each student should discuss on the discussion forum all the terms which could not be understood. This will improve his writing skills and enhance knowledge level about topics, which shall be immensely useful for end exam.  Appear several times, for all the Self-Tests, available for this course.  Student can use handouts for last minutes preparation just before end exam.

5. School of Science and Technology, Online Counseling Resource… © 2007, YCMOU. All Rights Reserved.5 Learning Objectives After studying this module, you should be able to:  Describe Protein Data bank.  How to Deposite Structure of protein.  Discuss Polices about External Data Deposition and Release.

6. School of Science and Technology, Online Counseling Resource… Introduction  The Protein Data Bank (PDB) at Brookhaven National Laboratory (BNL), is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules (Abola et al., 1987, 1997 ; Bernstein et al., 1977 ).  The archives contain atomic coordinates, citations, primary and secondary structure information, crystallographic structure experimental data, as well as hyperlinks to many other scientific databases.  Data are easily submitted via PDB's WWW-based tool AutoDep, in either mmCIF or PDB format  Data are most conveniently examined via PDB's WWW- based tool 3DB Browser.

7. School of Science and Technology, Online Counseling Resource… Protein Data Bank:1  Scientists around the world contribute structures to the PDB and use it on a daily basis.  The common interest shared by this community is a need to access information that can relate the biological functions of macromolecules to their three-dimensional structures.  The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids.proteinsnucleic acids  These data, typically obtained by X-ray crystallography or NMR spectroscopy.X-ray crystallographyNMR spectroscopy  The data is usually submitted by biologists and biochemists from around the world.biologists biochemists

8. School of Science and Technology, Online Counseling Resource… Protein Data Bank:2  These are released into the public domain, and can be accessed for free.public domain  The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB dataWorldwide Protein Data BankPDB  The PDB is a key resource in structural biology and is critical to more recent work in structural genomics.structural biologystructural genomics  PDB in terms of protein structure, protein function and protein evolution.protein structureprotein function protein evolution  The database stores information about the exact location of all atoms in a large biomoleculeatoms

9. School of Science and Technology, Online Counseling Resource… Protein Data Bank:3 The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan).RCSB PDB MSD-EBIPDBj The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National LaboratoryBrookhaven National Laboratory Management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB). Research Collaboratory for Structural Bioinformatics (RCSB)

10. School of Science and Technology, Online Counseling Resource… Protein Data Bank:4 The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease.RCSB The RCSB is a member of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniform data.wwPDB As of 26 September 2006, the database contained 39,051 released atomic coordinate entries (or "structures"), 35,767 of that proteins26 September2006  Data are stored in the mmCIF format specifically developed for the purpose.mmCIF

11. School of Science and Technology, Online Counseling Resource… Techniques for Structure Analysis:1  Rapid developments in the preparation of crystals of macromolecules and in experimental techniques for structure analysis and refinement have led to a revolution in structural biology.  These factors have contributed significantly to an enormous increase in the number of laboratories performing structural studies of macromolecules to atomic resolution and the number of such studies per laboratory. Advances include: 1.Recombinant DNA techniques that permit almost any protein or nucleic acid to be produced in large amounts; 2.Rapid protein and DNA (gene) sequencing techniques that have made protein sequencing routine;

12. School of Science and Technology, Online Counseling Resource… Techniques for Structure Analysis:2 3.Better X-ray detectors; 4.Real-time interactive computer graphics systems, together with more automated methods for structure determination and refinement; 5.Synchrotron radiation, allowing the use of extremely tiny crystals, multiple-wavelength anomalous dispersion (MAD) phasing, and time-resolved studies via Laue techniques; 6.NMR methods permitting structure determination of macromolecules in solution; and 7.Electron microscopy (EM) techniques, for obtaining high-resolution structures.

13. School of Science and Technology, Online Counseling Resource… PDB Archives:1  The archives contain atomic coordinates, bibliographic citations, primary and secondary structure information, as well as crystallographic structure factors and NMR experimental data.  Annotations in the structure entries include amino-acid or nucleotide sequences (with notes of any conflicts between the structure in the PDB and sequence databases), source organism from which the biological material was derived, references to papers, secondary structure, complexes with small molecules included within the structure, etc.

14. School of Science and Technology, Online Counseling Resource… PDB Archives:2  Third-party annotations include images and movies of structures, pointers to other databases which contain information on the structural class or family of the particular structure.

15. School of Science and Technology, Online Counseling Resource… Viewing the Data  The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML biomoleculesVMDRasMolPyMOLJmolMDL Chime QuteMolweb browserVRML  Plugin or any web-based software designed to visualize and analyse the protein structures such as STING.STING  A recent desktop software addition is Sirius. The RCSB PDB website also contains resources for education, structural genomics, and related softwareSirius

16. School of Science and Technology, Online Counseling Resource… Deposition at the Protein Data Bank  The Protein Data Bank (PDB) has long made available the experimental data which were used to determine the three- dimensional structures in the database.  In recent years more and more depositors and users of the PDB have come to appreciate the importance of reliable access to such fundamental data.

17. School of Science and Technology, Online Counseling Resource… Deposition at the Protein Data Bank  The deposition of the experimental data, along with the coordinates is essential for the following reasons. I.Rigorous validation of the structure- determination results can only be carried out using both atomic parameters and experimental structure-factor amplitudes. II. Archiving of this data will ensure their preservation and continued accessibility.

18. School of Science and Technology, Online Counseling Resource… Data Deposition and Release Policies  The RCSB PDB strongly encourages depositors to follow the guidelines set by the International Union of Crystallography [IUCr], National Institutes of Health [NIH], and the journals regarding submission of coordinate and experimental data.International Union of Crystallography  IUCr, the NIH, and the journals issued guidelines for the deposition and release of macromolecular coordinate and experimental data.  X-ray crystallographic results (atomic coordinates and structure factors) and NMR solution structure results (atomic coordinates and restraint files) should be deposited at the Protein Data Bank

19. School of Science and Technology, Online Counseling Resource… Data Deposition and Release Policies  All publications that describe macromolecular three-dimensional structures at the level of individual atomic positions must be accompanied by deposition of both the atomic coordinates and the structure-factor amplitudes in the appropriate database.  Authors are urged to release the atomic parameters and structure-factor amplitudes immediately after the publication date. This should be the normal practice.  They can, however, request a delay of up to six months in the release of the atomic parameter data and the structure-factor amplitudes

20. School of Science and Technology, Online Counseling Resource… Structure Deposition  At present more than 50% of the X-ray diffraction submissions are being deposited with their associated structure factors.  This increase in structure deposition is due to the ease of uploading the files via our WWW-based submission tool, AutoDep.  This tool is available both in the USA at BNL (PDB deposition site at http://www.pdb.bnl.gov/ ) and in Europe at the EBI (EBI deposition site at http://www2.ebi.ac.uk/pdb ).http://www.pdb.bnl.gov/ http://www2.ebi.ac.uk/pdb  The PDB strongly encourages all researchers to deposit their structure factors at the time of coordinate submission

21. School of Science and Technology, Online Counseling Resource… Standard mmCIF Format  In order to facilitate the use of deposited structure factors developed a standard interchange format for structure factors.  This standard is the mmCIF format, i.e. the IUCr- developed Macromolecular Crystallographic Information File. It was chosen for its simplicity of design and for being clearly self-defining.  The format is also easy to expand, as new crystallographic experimental methods or concepts are developed, by simply adding additional tokens.  The entire mmCIF crystallographic dictionary (http://ndb.rutgers.edu/NDB/mmcif ) has recently been ratified by the IUCr's COMCIFS committeehttp://ndb.rutgers.edu/NDB/mmcif

22. School of Science and Technology, Online Counseling Resource… PDB Program  The PDB has written a program to quickly and easily convert structure factors, as output by the most frequently used crystallographic programs, into the mmCIF format.  This tool, also converts binary CCP4 MTZ files, accessible through the AutoDep program following final testing.

23. School of Science and Technology, Online Counseling Resource… Validatation of Structure in PDB  The ready availability of structure-factor files in a standard format has made it possible for any scientist to validate a structure in the PDB versus its experimentally observed data.  There are now some excellent tools available for this, such as  SFCHECK (http://www.iucr.org/iucrtop/comm/ccom/Scho ol96/pdf/sw.pdf)http://www.iucr.org/iucrtop/comm/ccom/Scho ol96/pdf/sw.pdf  Uppsala Electron Density Server (http://alpha2.bmc.uu.se/valid/density/form1. html ).http://alpha2.bmc.uu.se/valid/density/form1. html

24. School of Science and Technology, Online Counseling Resource… PDB's Data Validation Checks  Based on these checks, authors may decide to give permission to release the entry immediately; to release it after up to a maximum one year hold; or go back and reexamine the structure in light of the output diagnostics before completing the submission procedure.  The PDB ID code is issued only after the author gives release approval

25. School of Science and Technology, Online Counseling Resource… PDB's Data Validation Checks ClassWhat is checked StereochemistryBond distances & angles, Ramachandran plot (dihedral angles), planarity of groups, chirality Bonded/non-bonded interactions Crystal packing, unspecified inter- and intraresidue links Crystallographic information Matthews coefficient, Z value, cell transformation matrices Noncrystallographic transformation Validity of noncrystallographic symmetry Primary sequence dataDiscrepancies with sequence databases Secondary structureGenerated automatically or visually checked heterogen groups Heterogen groupsIdentification, geometry and nomenclature Miscellaneous checksSolvent molecules outside the hydration sphere, syntax checks, internal data consistency checks

26. School of Science and Technology, Online Counseling Resource… Data Deposition Tools - 1  The following data deposition tools and instructions can make your structure deposition quick, easy, complete and accurate:  Preparation of structural data for deposition using pdb_extract1 and/or the desktop version of ADITpdb_extractdesktop version of ADIT  Preparation of structure factors for deposition using Crystallographic Data ValidationCrystallographic Data Validation  Validatation of structure using the Validation Server at RCSB PDB or the Validation Server at PDBjValidation Server at RCSB PDBValidation Server at PDBj

27. School of Science and Technology, Online Counseling Resource… Data Deposition Tools - 2  Deposition of structure using the structure deposition tool  beta-ADIT at RCSB PDBbeta-ADIT at RCSB PDB  ADIT at RCSB PDBADIT at RCSB PDB  ADIT at PDBj, ADIT at PDBj  Autodep at MSd-EBI.  Proper Instructions for X-ray crystallography structure depositions, NMR structure depositions, EM structure depositions and Electron diffraction, Fiber diffraction should be followed.

28. School of Science and Technology, Online Counseling Resource…

29. What You Learn…  You have learnt :  Different data deposition tools  PDB's data validation  Visualize the biomolecules with appropriate softwarebiomolecules

30. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Write a short note on Protein Data Bank ? 2.How to deposit Data to protein Bank ? 3.What is the prerequisite to submit Protein Data Bank © 2007, YCMOU. All Rights Reserved.30

31. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.Protein Data Bank 2.The deposition of the experimental data 3.PDB's data validation checks © 2007, YCMOU. All Rights Reserved.31

32. School of Science and Technology, Online Counseling Resource… Study Tips  Book Title: Protein Structure :Practical Approach Author: T.E. Creighton  Book Title: Protein structure Prediction Publisher : M.J.E. Sternberg

33. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia The Worldwide Protein Data Bank (wwPDB) — parent site to regional hosts (below)The Worldwide Protein Data Bank (wwPDB) RCSB Protein Data Bank - home pageRCSB Protein Data Bank MSD-EBI - home pageMSD-EBI Protein Data Bank Japan - home pageProtein Data Bank Japan A PDB Wiki - website for community annotationA PDB Wiki

34. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You !