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

2. SEP-SBI074-CP3-05 Introduction Programmes and Courses SEP –SBI074-CP3- U03

3. School of Science and Technology, Online Counseling Resource… Credits  Academic Inputs by Sonali Alkari Faculty YCMOU Nagpur Centre, Faculty LAD college P.G. D of Biotechnology Research officer Ankur Seeds Pvt Ltd sonalisa_alkari@yahoo.co.in Sonalisaal@rediffmail.com 3© 2008, YCMOU. All Rights Reserved.

4. School of Science and Technology, Online Counseling Resource… © 2008, 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… © 2008, YCMOU. All Rights Reserved.5 Learning Objectives  After studying this module, you should be able to : Describe molecular structure approach Discuss structural databank like pdb and csd.

6. School of Science and Technology, Online Counseling Resource… Molecular Structure  Implicit in the word "structure" is not only the concept of elementary units or parts, but also the interdependence and relationships of those parts to form a whole.  Molecular structure is the three-dimensional arrangement of atoms.  Three dimensional representations inform us about the interactions between different molecules and interactions between different parts of the same molecule.  It can thus be argued that modern science has adopted a structural approach to understanding the natural world, in which parts are defined and the interactions among them are explored. 6© 2008, YCMOU. All Rights Reserved.

7. School of Science and Technology, Online Counseling Resource… Structural Approach-1  In medicine, much of the progress in our ability to understand and treat disease can be seen to be a result of the structural approach.  Our continued probing of ever finer structural levels is leading to an increasingly sophisticated understanding of structure-function relationships, and the current pre-eminence of molecular biology is simply a logical extension of this progression.  As the level of structural analysis becomes finer, there is a corresponding increase in the amount of structural information. 7© 2008, YCMOU. All Rights Reserved.

8. School of Science and Technology, Online Counseling Resource… Structural Approach-2  A major part of the study of molecular structure is the description of the chemical bonds which are formed between atoms.  Structural informatics is a term coined by Jim Brinkley in 1991 to describe research related to representing and managing information about the physical organization of the body.  The field of structural biology research is concerned with elucidating molecular functions, the foundation for biological phenomena, through analysis of the 3-D structures of biomacromolecules. 8© 2008, YCMOU. All Rights Reserved.

9. School of Science and Technology, Online Counseling Resource… Structural Approach-3  Proteins are produced according to the genetic information coded in the genome, and serve as the key molecules in biological functions.  Genes, the 1-D information, are only able to exert their functionality when translated into 3-D information, i.e. proteins that possess a structure in space.  Thus, knowledge of proteins is integral to the understanding of biological processes.  Structural biology studies that provide information on 3-D protein structures, particularly studies utilizing synchrotron radiation that greatly expand the potential for understanding biological processes. 9© 2008, YCMOU. All Rights Reserved.

10. School of Science and Technology, Online Counseling Resource… In addition to providing information on protein functions, structural biology and structural genomics possess a high potential for contributing to the ‘early’ realization of genomic drug discovery (development of new drugs based on genome-related databases) and “tailor-made” medical care (drug prescriptions and medical treatments tailored to an individual's genetic background), and to help create solutions for environmental problems. Structural Approach-4 10© 2008, YCMOU. All Rights Reserved.

11. School of Science and Technology, Online Counseling Resource… Structural Database  The structural databases are the computer sites that organize, store and disseminate files that contain information consisting of structure of biomolecules.  Structural databases are the repository for 3- D structural data of proteins and nucleic acids.  These data, typically obtained by X-ray crystallography or NMR spectroscopy, are submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. © 2008, YCMOU. All Rights Reserved.11

12. School of Science and Technology, Online Counseling Resource… Why Structure Visualization  Proteins rely upon the shapes and properties of key functional areas of their three-dimensional structures to carry out biological functions.  The ability of protein to perform biological function depends on the formation of a three- dimensional structure (fold) that is stable in the normal environment of the protein.  We can predict secondary structure of a protein sequence whose structure and function are unknown.  Proteins in a family descend from a common ancestor and typically have similar three- dimensional structures, functions, and significant sequence similarity. 12© 2008, YCMOU. All Rights Reserved.

13. School of Science and Technology, Online Counseling Resource… Visulaization Tools  The vast majority of bioinformatics-specific tools shareware utilities developed with government funding, supplemented with a few dozen commercial offering.  Many tools are hardware or process-specific.  Visualization technologies, visualization tools leverage the pattern-recognition capabilities of the viewer's visual apparatus as opposed to logical, intellectual capabilities.  The selection of visualization tool should be a function of ease of use, power, speed, special features, cost, hardware requirements, documentation and support and overall functionality. 13© 2008, YCMOU. All Rights Reserved.

14. School of Science and Technology, Online Counseling Resource… Protein Data Bank:1  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 most conveniently examined via PDB's WWW-based tool 3DB Browser. 14© 2008, YCMOU. All Rights Reserved.

15. School of Science and Technology, Online Counseling Resource… Protein Data Bank:2  The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids.  These data, typically obtained by X-ray crystallography or NMR spectroscopy.  These are released into the public domain, and can be accessed for free.  The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data.  The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. 15© 2008, YCMOU. All Rights Reserved.

16. School of Science and Technology, Online Counseling Resource… Protein Data Bank:3  The database stores information about the exact location of all atoms in a large biomolecule.  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. © 2008, YCMOU. All Rights Reserved.16

17. School of Science and Technology, Online Counseling Resource… Protein Data Bank-4 © 2008, YCMOU. All Rights Reserved.17

18. School of Science and Technology, Online Counseling Resource… Cambridge Structural Database-1  The CCDC is dedicated to the advancement of chemistry and crystallography for the public benefit through providing high-quality information services and software.  The Cambridge Structural Database (CSD) is the principal product of the CCDC.  It is the central focus of the CSD System, which also comprises software for database access, structure vizualisation and data analysis, and structural knowledge bases derived from the CSD.  The CSD System also incorporates IsoStar, a knowledge base of intermolecular interactions, containing data derived from both the CSD and the PDB. 18© 2008, YCMOU. All Rights Reserved.

19. School of Science and Technology, Online Counseling Resource… Cambridge Structural Database-2 © 2008, YCMOU. All Rights Reserved.19

20. School of Science and Technology, Online Counseling Resource… Cambridge Structural Database-3  The CSD records bibliographic, chemical and crystallographic information for: organic molecules metal-organic compounds  whose 3D structures have been determined using: X-Ray diffraction neutron diffraction  The CSD records results of: single crystal studies powder diffraction studies 20© 2008, YCMOU. All Rights Reserved.

21. School of Science and Technology, Online Counseling Resource… What You Learn…  You have learnt : Molecular structure is the three-dimensional arrangement of atoms. The field of structural biology research is concerned with elucidating molecular functions, the foundation for biological phenomena, through analysis of the 3-D structures of biomacromolecules. The structural databases are the computer sites that organize, store and disseminate files that contain information consisting of structure of biomolecules. We can predict secondary structure of a protein sequence whose structure and function are unknown. PDB and CSD is a repository for 3-D structural data of proteins and nucleic acids. 21© 2008, YCMOU. All Rights Reserved.

22. School of Science and Technology, Online Counseling Resource… Critical Thinking Questions 1.Describe in details the structure approach. 2.Describe in details the Protein Data Bank. 3.Describe in details CSD. © 2008, YCMOU. All Rights Reserved.22

23. School of Science and Technology, Online Counseling Resource… Hints For Critical Thinking Question 1.The field of structural biology research is concerned with elucidating molecular functions, the foundation for biological phenomena, through analysis of the 3-D structures of biomacromolecules 2.The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. 1.The CSD comprises software for database access, structure vizualisation and data analysis, and structural knowledge bases derived from the CSD. © 2008, YCMOU. All Rights Reserved.23

24. School of Science and Technology, Online Counseling Resource… Study Tips:1  Book1 Title: Molecular Cell Biology Author: Harvey Lodish, David Baltimore Publisher: W. H. Freeman and Company  Book2 Title: Principles of Biochemistry Author: AlbertL Lehninger Publisher: CBS Publishers & Distributors 24© 2008, YCMOU. All Rights Reserved.

25. School of Science and Technology, Online Counseling Resource… Study Tips:2  Book3 Title: Biochemistry Author: Lubert stryer Publishers: Freeman International  Book4 Title: Biochemistry Author: Keshav Trehan Publishers: Wiley Eastern 25© 2008, YCMOU. All Rights Reserved.

26. School of Science and Technology, Online Counseling Resource… Study Tips www.en.wikipedia.org Microsoft Encarta Encyclopedia http://en.wikipedia.org/wiki/ Wikipedia the free encyclopedia 26© 2008, YCMOU. All Rights Reserved.

27. School of Science and Technology, Online Counseling Resource… End of the Presentation Thank You 27© 2008, YCMOU. All Rights Reserved.