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Molecular Biophysics Unit

http://mbu.iisc.ernet.in/courses.htm

MOLECULAR BIOPHYSICS UNIT


Indian Institute of Science, Bangalore, India
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Courses offered during August Term

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MB 201 (AUG) 2:0


Introduction to Biophysical Chemistry
RAGHAVAN VARADARAJAN

Basic thermodynamics, ligand binding and co-operativity in biological systems, kinetics, diffusion and sedimentation. Tinoco, I, Sauer K, Wang J C Physical Chemistry, Principles and Applications in Biological Sciences Prentice Hall, New Jersey, USA, 1978. Cantor, C.R., and Schimmel P.R., Biophysical Chemistry, Vols. I-III, W.H. Freeman and Co., San Francisco, USA, 1980.

MB 204 (AUG) 3:0


Molecular Spectroscopy and Structure
P. BALARAM AND SIDDHARTHA P. SARMA

Elementary ideas of bonding and structure, stereochemistry electronic (UV/visible) spectroscopy, fluorescence spectroscopy, vibrational spectroscopy (IR/Raman), optical rotatory dispersion and circular dichroism (ORD/CD). Nuclear magnetic resonance and mass spectrometry. Chemical and biological applications.

MB 205 (AUG) 2:0


Introduction to X-ray Crystallography.
M. VIJAYAN and K. SUGUNA Crystal morphology and symmetry. Symmetry elements and symmetry operations, point groups, lattice space groups. Production and properties of X-rays, diffraction of X-rays by crystals, Laue equations, Bragg'sLaw, Fourier transformation and structure factor, reciprocal lattice, experimental techniques, rotating crystals and moving film methods. Basic ideas of structure determination, Patterson and Fourier methods, chemical crystallography, structures of organic, inorganic compounds and minerals, powder diffraction. Buerger M.J., Elementary Crystallography Woolfson M.M., An Introduction to X-ray Crystallography. Stout H. and Jenson L.H., X-ray Structure Determination, Macmillion, 1968. Go Top

MB 206 (AUG) 3:0


Conformational and Structural aspects of biopolymers.
M. BANSAL, S. VISHVESHWARA AND N. SRINIVASAN

Basic ideas on structure and conformation of simple molecules structural features of proteins, nucleic acids and

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Molecular Biophysics Unit

http://mbu.iisc.ernet.in/courses.htm

carbohydrates, aspects of biomolecular forces . Higher order structural organisation of proteins and nucleic acid. Ramachandran, G.N., and Sasisekharan, V. Advances in Protein Chemistry, Vol. 23, Academic Press, P. 283 (1968). A.R. Leach, Molecular Modelling : Principles and Applications, Prentice Hall (2001). Schulz and Schirmer, Principles of Protein Structure, Springer-Verlag (1979).

MB 207 (AUG) 2:0


DNA-Protein interaction, Regulation of gene expression, Nanobiology.
DIPANKAR CHATTERJI Basic concepts on structural basis for macromolecular recognition; concept of charge in macromolecules; specific and non-specific recognition; symmetry in DNA-protein recognition; structural ensembles; co-operativity; specific examples; story of lambda; restriction enzyme recognition; t-RNA synthetase recognition; promoter-RNA polymerase interaction; inducers and repressors; action at a distance; single molecular paradigm; methods to follow nanobiology; DNA-protein recognition at the level of single molecules. Genes IX, Benjamin Lewin, Oxford. Transcriptional Regulations I and II, McWright and Yamamoto, Cold Spring Harbor. A Genetic Switch, Mark Ptashne, Cell Press. Genes & Signals, Cold Spring Harbor Laboratory Ptaschne and Gann. Selected papers.

MB 209 (AUG) 2:0


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Molecular Basis of Signal Propagation and Synaptic Transmission in Neurons.


S. K. SIKDAR AND RISHIKESH NARAYANAN

Membrane components and structures; membrane transport; passive and active electrical properties of the membrane-ionic mechanisms of membrane and action potential; quantifying ionic hypothesis by voltage-clamp technique; Hodgkin Huxley formalism; structure-function aspects of voltage and chemically gated ionic channels; excitatory and inhibitory postsynaptic potentials; patch-clamp technique; recording and analysis of electrophysiological data; measurement of Ca concentrations in single cells; cell membrane capacitance and exocytosis, confocal microscopy. Synaptic plasticity: short-term and long-term potentiation and depression; mechanisms underlying synaptic plasticity; dendritic structure; dendritic ion channels; active properties of dendrites; dendritic spikes and backpropagating action potentials; intrinsic plasticity; mechanisms underlying intrinsic plasticity.

Reference books: Hille, B., Ionic channels of excitable membranes. 2nd Edition, Sinauer Associates, Sunderland, Massachussets. Rudy, B., and Iverson, L.E. (Eds.) Methods in Enzymology, 207, 1992. Kandel, E.R., Schwartz, J.H., & Jessel, T.M., Essentials of Neural Science and Behaviour, Prentice Hall International, 1995. Cowan, W.M., Sudhof, T.C., Stevens, C.F., Synapses, The Johns Hopkins University Press, First edition, 2003. Stuart, G., Spruston, N., Hausser, M., Dendrites, Oxford University Press, Second edition, 2008.

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Courses offered during January Term

MB 301 (JAN) 2:0


Protein Structure, Folding and Design.
P. BALARAM Polypeptide and protein conformations. Organisation of secondary structure elements in proteins. Structural motifs and analysis of information from the data bank of protein crystal structures. Folding pathways and experimental approaches to the protein folding problem. Random and self directed mutagenesis as a tool in understanding protein structure and folding. Protein engineering and the design of new proteins. Go Top

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Molecular Biophysics Unit

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MB 302 (JAN) 3:0


Macromolecular Crystallography.
M.R.N. MURTHY

Review of crystallographic concepts, protein crystallization, oscillation photography, data processing, isomorphous replacement, anomalous dispersion, multi wavelength methods, molecular replacement, refinement, model building, quality assessment, analysis and documentation. Reference books: Principles of Protein X-ray Crystallography, J Derenth, Springer Practical Protein Crystallography, Duncan E.Mc Ree, Elsevier Crystallography made crystal Clear, Gale Rhodes, Wiley Outline of Crystallographyy for Biologists, David Blow, Oxford University Press

MB 303 (JAN) 3:0


Elements of Structural Biology.
B. GOPAL

Elements of structural biology. Methods for determining structures of biological macromolecules, biophysical and biochemical methods to better understand structural data, proteomic tools to examine cellular protein composition. Reference books: Kensal, E. Van Holde et al., Principles of Physical Biochemistry (Second Edition) Pearson Education International Cantor, C.R., and Schimmel P.R., Biophysical Chemistry, Vols. I-III, W.H. Freeman and Co., San Francisco, USA, 1980 Research papers and reviews. Go Top

MB 305 (JAN) 3:0


Biomolecular NMR Spectroscopy.
SIDDHARTHA P. SARMA Basic theory of NMR spectroscopy. Classical and theoretical descriptions of NMR spectroscopy. Product operator formalism for description of multipulse homonuclear and heteronuclear NMR experiments. Multidimensional NMR spectroscopy. Description of basic homonuclear two dimensional NMR experiments useful for structure determination of biological macro-molecules. Experimental aspects of homonuclear NMR spectroscopy: data acquisition, processing and interpretation of 2D homonuclear spectra. Principles of heteronuclear NMR spectroscopy. Analysis of 3D and 4D heteronuclear isotope edited NMR pulse sequences. Introduction to relaxation and dynamic processes (chemical and conformational processes) that affect NMR experiments. Reference books: Protein NMR Spectroscopy Principles and Practice J. Cavanaugh, Fair Brother, A.G. Palmer III & N. Skelton (1995), Academic Press. Spin Dynamics - .M. Levitt (2000) John Wiley. NMR of Proteins & Nucleic Acids Kurt Wuthrich, John Wiley (1986).

MB 208 (JAN) 3:1


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Theoretical and computational neuroscience


RISHIKESH NARAYANAN AND ARUN SRIPATI

Need for and role of theory and computation in neuroscience; various scales of modeling; ion channel models; single neuron models; network and multiscale models; models of neural plasticity; oscillations in neural systems; central pattern generators; single neuron oscillators; oscillators as nonlinear dynamical systems; information representation; neural encoding and decoding; population codes; hierarchy and organization of sensory systems; receptive field and map modeling; case studies, computational laboratory and projects. Prerequisites: MB209 (or basic exposure to ion channels and their functions), basic knowledge of linear algebra, probability, statistics and ordinary differential equations, and some programming knowledge.

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Molecular Biophysics Unit

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Books and references a. Peter Dayan and L. F. Abbott, Theoretical Neuroscience: Computational and Mathematical Modeling of Neural Systems, The MIT press, 2005. b. Christof Koch and Idan Segev (Eds), Methods in Neuronal Modeling: From Ions to Networks, The MIT press, second edition, 1998. c. Eric De Schutter (Ed.), Computational modeling methods for neuroscientists, The MIT press, 2009. d. Eugene Izhikevich, Dynamical systems in neuroscience: the geometry of excitability and bursting, The MIT press, 2006. e. Kenji Doya, Shin Ishii, Alexandre Pouget, Rajesh PN Rao (Eds), Bayesian Brain: Probabilistic Approaches to Neural Coding, The MIT press, 2007

DB 201 (JAN) 3:0


Mathematics and Statistics for biologists.
N.SRINIVASAN , N.V.JOSHI AND K.SEKAR Functions; co-ordinate systems; complex algebra vectors matrices, determinants; linear equations; series; limits; integrals; derivative techniques of calculus power series; trigonometric series; frequency distributions; central tendency; variability; correlation prediction and regression statistical methods and tests.

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Molecular Biophysics Unit, IISc, Bangalore, India

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