Protein Engineering Techniques: Gateways to Synthetic Protein Universe PDF
Preview Protein Engineering Techniques: Gateways to Synthetic Protein Universe
SPRINGER BRIEFS IN APPLIED SCIENCES AND TECHNOLOGY FORENSIC AND MEDICAL BIOINFORMATICS Krishna Mohan Poluri Khushboo Gulati Protein Engineering Techniques Gateways to Synthetic Protein Universe SpringerBriefs in Applied Sciences and Technology Forensic and Medical Bioinformatics Series editors Amit Kumar, Hyderabad, India Allam Appa Rao, Hyderabad, India More information about this series at http://www.springer.com/series/11910 Krishna Mohan Poluri Khushboo Gulati (cid:129) Protein Engineering Techniques Gateways to Synthetic Protein Universe 123 Krishna MohanPoluri Khushboo Gulati Department ofBiotechnology andCenter Department ofBiotechnology forNanotechnology Indian Institute of Technology Roorkee Indian Institute of Technology Roorkee Roorkee,Uttarakhand Roorkee,Uttarakhand India India ISSN 2191-530X ISSN 2191-5318 (electronic) SpringerBriefs inApplied SciencesandTechnology ISSN 2196-8845 ISSN 2196-8853 (electronic) SpringerBriefs inForensicandMedical Bioinformatics ISBN978-981-10-2731-4 ISBN978-981-10-2732-1 (eBook) DOI 10.1007/978-981-10-2732-1 LibraryofCongressControlNumber:2016954620 ©TheAuthor(s)2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. 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Theregisteredcompanyaddressis:152BeachRoad,#22-06/08GatewayEast,Singapore189721,Singapore Dedicated to all our teachers and mentors for their invaluable guidance and unconditional support throughout our research careers Krishna Mohan Poluri Khushboo Gulati Preface Proteins are the string of amino acids that play key roles in almost all the physi- ological and pathological events that are occurring in the body. Functionality of proteinsisdirectlyrelatedtothestructuretheyattain,whichultimatelydependson the composition of their unique amino acid sequence. Protein engineering is a fledging field and a creative process to design the target proteins or signaling networks with desirable structure andfunctions. The idea of proteinengineering is to utilize the unexplored sequence space in order to design/rewire the proteins as per human wish and for the well-being of the society. Numerous protein engi- neering methods have been developed that are aiding in various research and technologicalapplications.Indeed, proteinengineeringhasbeenapowerfultoolin bioengineering for last couple of decades and has generated vast number of useful enzymes/proteinsthathavephenomenaltherapeuticandindustrialpotential.Protein engineering field started gaining its approval for last couple of years: In 2012, the market is $56 billion and expected to increase to 168 billion in 2017, at a Compound Annual Growth Rate (CAGR) of 10.9 % from 2012 to 2017. In this brief, we primarily focus on most popular experimental methods and several computational programs that are being widely used under the categories of directed evolution, rational and de novo designing of proteins and their biotechnological/biomedical applications. Further, the brief sheds light on the advantagesandpitfallsoftheexistingmethodologiesandtheirfutureperspectives. Thebookisdividedintofivechapters:Chapter1describesthefundamentalaspects of protein structure–function–folding relationships and an introduction to the field ofbiomolecularandproteinengineeringtechniques.Chapter2summarizesvarious experimental techniques that are used for generating novel proteins under the framework of directed evolution. Chapter 3 provides an overview of all the com- putational methods that aids us in understanding structure–function relationships through a rational approach. Chapter 4 highlights the protocols of de novo protein designing and combinatorial or computer-aided directed evolutionary approaches for engineering novel scaffolds. Chapter 5 provides a glimpse of several biotech- nologicalandbiomedicalapplicationsoftheengineeredproteinsthataregenerated using the techniques described in Chaps. 2–4. vii viii Preface Weanticipatethatthisbriefwillprovideabroaderperspectiveaboutthefieldof protein engineering to all the researchers planning to gain comprehensive under- standing and an up-to-date knowledge about the fundamental techniques and their biotechnological/biomedical applications. Roorkee, India Krishna Mohan Poluri Khushboo Gulati Acknowledgements KMP greatly acknowledges the support DBT-IYBA fellowship (BT/07/IYBA/ 2013-19),SERBYoungScientistgrant(SERB-SB/YS/LS-380/2013),andMHRD- IITR Faculty Initiation Grant (FIG-BIO-637), from Government of India (GoI). KG acknowledges the support MHRD-Assistantship for pursuing Ph.D. at IIT- Roorkee. ix Contents 1 World of Proteins: Structure-Function Relationships and Engineering Techniques.... .... .... .... .... .... ..... .... 1 1.1 Introduction ... .... ..... .... .... .... .... .... ..... .... 1 1.2 Functional Characteristics of Proteins. .... .... .... ..... .... 2 1.3 Transfer of Genetic Information: From DNA to Proteins ... .... 3 1.4 Amino Acids, Building Blocks of Proteins. .... .... ..... .... 6 1.4.1 Non Polar Amino Acids ... .... .... .... ..... .... 6 1.4.2 Charged Polar Amino Acids .... .... .... ..... .... 6 1.4.3 Uncharged Polar Amino Acids .. .... .... ..... .... 7 1.5 Hydrophobicity Profiles of Amino Acids .. .... .... ..... .... 7 1.6 Acidic and Basic Properties of Amino Acids... .... ..... .... 7 1.7 Structural Organization of Proteins... .... .... .... ..... .... 7 1.7.1 Primary Structure. .... .... .... .... .... ..... .... 8 1.7.2 Secondary Structure... .... .... .... .... ..... .... 8 1.7.3 Tertiary Structure. .... .... .... .... .... ..... .... 11 1.7.4 Quaternary Structure .. .... .... .... .... ..... .... 12 1.8 Motifs/Super Secondary Structures... .... .... .... ..... .... 13 1.9 Protein Stability .... ..... .... .... .... .... .... ..... .... 16 1.9.1 Ionic Interactions. .... .... .... .... .... ..... .... 16 1.9.2 Van der Waal Interactions.. .... .... .... ..... .... 16 1.9.3 Hydrophobic Interactions... .... .... .... ..... .... 17 1.10 Protein Denaturation, Renaturation and Folding Energy Landscape. .... .... ..... .... .... .... .... .... ..... .... 17 1.11 Structure Determination of Proteins .. .... .... .... ..... .... 19 1.11.1 X-Ray Crystallography .... .... .... .... ..... .... 20 1.11.2 Nuclear Magnetic Resonance Spectroscopy (NMR).... ..... .... .... .... .... .... ..... .... 20 1.12 Concept of Biomolecular and Protein Engineering... ..... .... 21 References.. .... .... .... ..... .... .... .... .... .... ..... .... 23 xi
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