��������������� BS400 Molecular Biophysics BT808 Principles of Biomolecular Interaction and Recognition Course material will be made available on moodle moodle.iitb.ac.in
��������������� Objective To learn about the factors that are responsible for the conformation and assembly of biomolecules and recognition and interactions of biomolecules EMPHASIS Manifestation in biological systems Current status and limitations Recent and classic examples
��������������� This course vis-à-vis others in the curriculum An imaginary hybrid of telescope and microscope We see things differently when we change the depth of focus vis-a-vis (meaning from an online dictionary): (1) in relation to (2) as compared to Prof. Sudesh Balan, IDC, IIT Bombay: Depth of Focus video
��������������� Outline 1. Sequence - {Folding} - Structure - Dynamics - Function paradigm: perspective for the course 2. Molecular structure: representation, conformational changes, conformational ensembles, conformer selection 3. Steric effect or hard-sphere approximation: preferred (allowed) versus not-preferred (disallowed) conformations; application to monosaccharides and peptides; Ramachandran map ... continued paradigm (meaning from online dictionaries): (1) The generally accepted perspective of a particular discipline at a given time (2) A framework within which theories, laws, and generalizations and the experiments performed in support of them are formulated
��������������� Outline 4. Non-covalent interactions: types, relative strengths, examples (from biological systems) of their manifestation and consequences 5. Entropy: standard entropy of approximation, entropic and enthalpic cooperativities, enthalpy-entropy compensation, hydrophobic effect, conformationally constrained molecules and protein design 6. Stability and folding of proteins: measuring conformational stability, theories of protein folding, φ φ value analysis φ φ 7. Lipids: phase transitions 8. Binding: Specificity and affinity
��������������� Reading material Books Recent editions of general Biochemistry books include ■ a chapter on non-covalent interactions in Biology ■ structural aspects of biomolecules Important Spend at least 30-45 minutes after EVERY class Go through slides / any points you might have noted down, • Form small groups and discuss • Make an attempt to write down in a few “bullet points” the • concepts discussed or key points conveyed or “take home message” of that class Clarify doubts either in the next class or in person ASAP •
��������������� “Extra” reading material 1. Books Proteins. Structure and molecular properties by Creighton Structure in proteins by Kyte 2. Original research papers and review articles Will give you the reference when we discuss the paper
��������������� Holidays and “adjustments” this semester... 1. Friday January 6 - at scheduled time (KReSIT Seminar Hall, 3 rd floor) 2. Tuesday March 20 - Friday time-table 1. Friday February 10 2. Friday March 23 3. Wednesday April 4 - Thursday time-table 4. Friday April 6
��������������� Evaluation for BS400 26 th or 28 th Jan. Quiz 1 15 marks Mid-sem. 30 marks February 20-25, 2012 23 rd or 24 th March Quiz 2 15 marks End-sem. 40 marks April 20-May 2, 2012
��������������� Evaluation for BT808 26 th or 28 th Jan. Quiz 1 10 marks Mid-sem. 30 marks February 20-25, 2012 23 rd or 24 th March Quiz 2 10 marks 2 nd week of April Paper presentation 10 marks End-sem. 40 marks April 20-May 2, 2012
��������������� Outline 1. Sequence - {Folding} - Structure - Dynamics - Function paradigm: perspective for the course 2. Molecular structure: representation, conformational changes, conformational ensembles, conformer selection 3. Steric effect or hard-sphere approximation: preferred (allowed) versus not-preferred (disallowed) conformations; application to monosaccharides and peptides; Ramachandran map ... continued
��������������� Importance of structure in Biology 2009 Ribosome V Ramakrishnan, T A Steitz, A E Yonath 2003 Channels P Agre, R Mackinnon 2002 NMR methods K Wuethrich (0.5) 1991 NMR methods R R Ernst 1988 Photosynthetic RC J Deisenhofer, R Huber, H Michel 1985 X-ray direct methods H A Hauptman, J Karle 1982 X-ray electron microscopy A Klug 1974 Statistical mechanics P J Flory 1969 Concept of conformation D H R Barton, O Hassel 1966 Molecular orbital methods R S Mulliken 1964 X-ray, 3D structures D C Hodgkin 1962 X-ray, 3D structures M F Perutz, J C Kendrew 1958 Structure of insulin F Sanger 1962 Structure of DNA F H C Crick, J D Watson, M H F Wilkins
��������������� Sequence - Folding - Structure Campylobacter jejuni PglD (an acetyltransferase) GSAMARTEKIYIYGASGHGLVCEDVAKNMGYKECIFLDDFKGMKFESTLPKYDFFI AIGNNEIRKKIYQKISENGFKIVNLIHKSALISPSAIVEENAGILIMPYVVINAKA KIEKGVILNTSSVIEHECVIGEFSHVSVGAKCAGNVKIGKNCFLGINSCVLPNLSL ADDSILGGGATLVKNQDEKGVFVGVPAKRM PDB id 3BSY (chain A) different views of the same structure
��������������� Sequence - {Folding} - Structure Cyclin dependent kinase inhibitor p21 (SwissProt accession no. P38936.3) MSEPAGDVRQNPCGSKACRRLFGPVDSEQLSRDCDALMAGCIQEARERWNFDFVTE TPLEGDFAWERVRGLGLPKLYLPTGPRRGRDELGGGRRPGTSPALLQGTAEEDHVD LSLSCTLVPRSGEQAEGSPGGPGDSQGRKRRQTSMTDFYHSKRRLIFSKRKP 3D structure ? Intrinsically disordered protein Natively unstructured protein “folds” after it interacts with and binds to its target May fold differently on binding to different targets J. Mol. Graphics Model. (2001) 19:26
��������������� Static versus dynamic Still picture (a photograph) versus a video clip http://mjfredrick.files.wordpress.com/2011/03/ http://conservativetshirts.info/wp- harry-potter-with-wand-wallpaper.jpg content/uploads/2011/09/harry-potter- giveaway-LA-11-15-101.jpg
��������������� Sequence - Folding - Structure - Dynamics Lactobacillus casei dihydrofolate reducatase PDB id 2LF1
��������������� Mechanics at work http://image.shutterstock.com/display_pic_with_lo http://mantivities.files.wordpress.com/ go/84324/84324,1169286790,1/stock-photo-auto- 2008/09/mechanic.jpg mechanic-working-under-the-car-2517812.jpg
��������������� Conformational changes www.nature.com/nature/journal/v432/n7015/fig_tab/nature02981_F6.html Nature (2004) 432:361
��������������� Conformational changes PROTEIN Unfolded Folded ? Human lysozyme PDB id 3FE0
��������������� Conformational changes PROTEIN Unfolded Partially folded states Folded Sodium lauroyl sarcosinate-bound Nuclear co-activator binding domain of CREB-binding protein α -synuclein α α α PDB id 2KKW (CREB: cAMP response element binding) PDB id 2KKJ
��������������� Conformational changes RNA Unfolded Folded ? Bacillus subtilis yitJ S Box/SAM-I Riboswitch PDB id 3NPB
��������������� Conformational changes ��������������� 4 C 1 - α 1 C 4 - α 2 S O - α α -L-idopyranose α -L-idopyranose α -L-iduronopyranose α α α α α α -OH - equatorial -CH 2 OH - axial -OH - axial -COOH - equatorial -OH - equatorial -CH 2 OH - equatorial
��������������� Valley between two mountains, a water well?
��������������� Energy landscape of a protein well defined “minimum energy” or “stable” state Intrinsically Folded protein disordered Curr. Opin. Struct. Biol. (2011) 21:426
��������������� Sequence - Folding - Structure - Dynamics - Function E c MbCO Myoglobin (Mb): State Mb, MbCO, or MbO 2 cc E c : potential energy cc: conformational coordinates Science (1991) 254:1598
��������������� Conformational ensembles PROTEIN May contain May contain “correctly” folded inactive or active Unfolded Folded (inactive or active) forms or misfolded forms Helicobacter pylori SlyD PDB id 2KR7 ensemble: a group producing a single effect
��������������� Sequence - Folding - Structure - Dynamics - Function E c MbCO Myoglobin (Mb): State Mb, MbCO, or MbO 2 cc E c MbCO: different states (low temp flash photolysis) A 0 A 1 A 3 Different states: stretching of bound CO different (IR) Tier 0 Rate of binding CO: different (A 0 , fastest; A 3 , slowest) Regulation by switching between different states cc0 Energy landscape of myoglobin E c : potential energy cc: conformational coordinates
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