Biol 2012 Exploring Proteins PDF

Biol 2012 Exploring Proteins Jörn Werner 1  Exploring Proteins Overview Structure and Activity of Proteins – architecture, protein interactions, enzymes, glycosylation (post-translational modification) – Important proteins haemoglobin, and antibodies. enzymes, ca...

Biol 2012 Exploring Proteins Jörn Werner 1  Exploring Proteins Overview Structure and Activity of Proteins – architecture, protein interactions, enzymes, glycosylation (post-translational modification) – Important proteins haemoglobin, and antibodies. enzymes, catalytic functions, multi enzyme complexes, proteases and lipases membrane proteins Proteomics Study of the whole complement of proteins in a cell 2  Who is teaching what… Dr. Jörn Werner Dr. Matthew Dr. Joel Allen Protein Architecture Bellamy Glycobiology and Interactions Protein Structure and Function Dr. Ivo Tews Dr. Rob Ewing Dr. Phil Williamson Proteomics Membrane Proteins Enzymes Exploring Proteins Course Format Lectures Computer based questionnaires (5%) – On Blackboard; observe submission dates! Portrait of a Protein / Library Project (25%) – Sign-up for your chosen protein on blackboard – Consult information on blackboard site! – Submission deadline is Fri 28th March – Chimera Help desk in you timetable (week 2-6) Feedback – Computer questionnaires – Library project (written and option for oral feedback) – Lectures provide feedback on specific questions 4 If you have an issue with the module who can you talk to? There are many options: 1. Talk to / or email the lecturer directly 2. Email the Module Coordinator ([email protected]) 3. Provide comments / issues / improvements to your SR for the Student Staff Liaison Committee (SSLC) meeting 4. Email the Director of Student Experience 5. Complete the Module Evaluation Questionnaire (end of semester)  Textbooks Williamson, M. (2011): How Proteins Work, Garland, NY This is an excellent and recent textbook on the subjects covered in the course. General Biochemistry books with excellent sections on protein structure are: 1) Voet, Biochemistry (2011) (4th edition) Wiley, NY 2) Berg, Tymoczko and Stryer (2007) Biochemistry (6th edition) Freeman, NY 3) Lodish et al. (2004) Molecular cell Biology (5th edition) Freeman, NY 4) Lehninger (2008) Principles of Biochemistry, Freeman, NY More focused textbooks: 1) Branden Tooze: Introduction to Protein Structure (2nd edition) Garland, NY 2) Creighton: Proteins, Structures and Molecular Properties, Freeman, NY 3) Alan Fersht (1999) Structure and Mechanism in Protein Science: A guide to enzyme catalysis and protein folding (3rd edition) W.H.Freeman, New York 4) Mary Luckey (2008) Membrane Structural Biology, Cambridge University Press 6  Library Project: Portrait of a Protein Membrane proteins: 1) Potassium channel KcsA or KvAP 2) Bacteriorhodopsin (Br) Globular proteins: 3) Catalase 4) human serum albumin 5) Calmodulin 6) Green fluorescent protein 7) Major histocompatibility complex I (MHC I) 8) Small signalling G-proteins (ras family) 9) Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 S) 10) Adenomatous Polyposis Coli (APC)  Portrait of a Protein Questions you may consider: What is the function of the protein in question? How does the structure inform you about the function? Have you described the structure? Does the protein require any processing to reach its final, functional form? Is it functional as a single polypeptide, or is it a dimer, trimer etc.? Is it a singular gene product or are there multiple isoforms of the protein? Is its function/activity regulated at the protein and/or gene level? Can specific residues or precise structural regions be mapped to specific aspects of its function or regulation? Are there any mutations (disease-related or engineered in) that shed light on the role of specific residues?  Library Project: Portrait of a Protein Choose protein from the list (on blackboard) Write a review (5 pages) including at least three figures you made yourself (e.g. with UCSF chimera) using the atomic coordinates of the protein Use the template document given on blackboard Chimera help desk available weeks 2-8 (see timetable) Abigail Sudol will support you. Deadline Fri 28th March 4pm More information and templates as well as software guides are on blackboard under Structural Biology is evolving Insulin monomer Insulin Receptor complex  Proteins move: They are molecular machines Movie of the Ribosome at work https://youtu.be/q_n0Ij3K_Ho 11 https://www.nobelprize.org/prizes/chemistry/2009/illustrated-information/ Atomic structure(s) of a whole cell 12 Kuehner 2009, Science 326, 1235  Protein Science: A Nobel Subject “for the development of methods 2002 for identification and structure analyses of biological macromolecules” Fenn Tanaka Wüthrich “for discoveries 2003 concerning channels in cell membranes” Agre MacKinnon “molecular basis R. Kornberg of eukaryotic 2006 transcription“ "for the discovery and development of the green 2008 fluorescent protein, GFP" 13 Shimomura Chalfie Tsien  Protein Science: A Nobel Subject "for studies of the structure and 2009 function of the ribosome" Ramakrishnan Steitz Yonath “for studies of G-protein- 2012 coupled receptors" Lefkowitz Kobilka "for the development of multiscale models for complex 2013 chemical systems". Warshel Karplus Levitt "for developing cryo-electron 2017 microscopy for the high-resolution structure determination of biomolecules in solution" 14 Dubochet Frank Henderson Go to: http://www.nobelprize.org/  Protein Science: A Nobel Subject The Nobel Prize in Chemistry 2024 was divided, one half awarded to David Baker "for computational protein design", the 2024 other half jointly to Demis Hassabis and John Jumper "for protein structure prediction" Baker Hassabis Jumper 15  Protein Structure Prediction Holy Grail of Structural Biology In 2021 saw the publication of a novel computer algorithm that predicts 3D protein structures from sequence only (ab-initio structure prediction) 16 AlphaFold It is so efficient that one can predict all protein structures of entire organisms. Eg human is done https://alphafold.ebi.ac.uk/ Jumper, J et al. Highly accurate protein structure prediction with AlphaFold. Nature (2021).  Designer Proteins De novo structures Design of Enzymes TOP7: Designed e.g. Substrate structure specificity Cheng-Yu, C Kuhlman, B (2003). (2009) PNAS Science. 302 1364 106:3764 Designing interactions Membrane Proteins affinity and specificity – Pore size design e.g. – selectivity Cytokine IL2/super IL2 Chowdrhury, R (2018) Nat Silva DA, (2023) Commun 9, Nature 565,186 3661 Exciting Times in Protein Science: many genomes are sequenced Evolution E.g. Cancer Gene map Understand biology Study diseases 18  Green Fluorescent protein Cells Brain tissue Aequorea victoria discover apply apply engineer understand 19 A Protein may exist in several states 20  3D structure is encoded in the amino acid sequence 1) Oxidation under denatured conditions leads to formation of wrong disulfide bonds 2) However re-naturation first and then oxidation leads to correct disulfide bonds => Amino acid sequence on its own encodes correct three dimensional 21 structure of a protein Single protein domains typically undergo an all or nothing (2-state) folding process 22 Progression to the folded state: Protein Folding Funnel Unfolded protein: many configurations many interactions between residues but few native like interactions Transition state: many contacts & key residues have native contacts (c.f. yellow spheres) Native state: many interactions, all are native interactions 23 CM. Dobson (2003) Nature 426, 884-890 A Protein may exist in several states 24  Misfolding can cause disease Classic definition of an infectious agent required DNA or RNA ( as information stores) to allow replication in the host Prion is an infectious agent entirely composed of protein Prp Prion cause BSE (mad cow’s disease) CJD in humans scrapie in sheep 25 Mechanism of Prp replication Prpsc misfolded form of Prpc 26 Differences: Prpc and PrPsc Structure of C-terminal PrPsc: richer in b-strand domain of PrPc 27  Many protein have been shown to undergo misfolding associated with disease … Common feature is the formation of amyloid deposits 28 Chiti etal (2006) Annu.Rev.Biochem 75, 333 Misfolded fibers (amyloid) have common b-structure Fibril axis Electron micrograph of Amyloid beta fibres with fibre reconstruction 29 Amyloid fibre formation appears to have a common mechanism 30  Summary Structural Biology is – central to almost all aspects of biology – an evolving field: study single proteins to entire organisms Proteins may function in more than one structural state – protein misfolding may cause disease 31