Molecular Biophysics - Course Descriptions

Covers partial differential equations, statistical methods, matrix formulations, sets of integrodifferential equations, and kinetic equations with specific problems chosen for analysis selected for relevance to research now in progress in the Molecular Biophysics and Neuroscience Programs.

Covers optical spectroscopy with emphasis on applications in biomedical research. including interaction of light and matter, absorption spectroscopies (UV/vis and infrared), fluorescence, and circular dichroism.

The basics of computational methods used to analyze protein sequences and structures. Topics include sequence similarity searches using profile-based tools, functional prediction, structure prediction and threading, homology modeling, energy-based simulations, protein classification, and evolutionary concepts: homology inference and tree reconstruction.

Biological signal transduction networks are characterized by complexity: combinatoric incoming and intracellular signals, combined slow and fast responses, interlocking pathways, adaptive responses, feedback controls, etc. Computational Modeling provides an introduction to computational analytical approaches, modeling strategies and other quantitative techniques for understanding cellular signaling networks beginning with simple kinetic, equilibrium and probabilistic approaches to studying individual regulatory pathways. These strategies are then extended to describe complex systems using both deterministic and stochastic methods and includes examples chosen to stress analysis, evaluation and interpretation of experimental data in real signaling systems.

Introduction to the principles of nuclear magnetic resonance (NMR), emphasizing its application to macromolecular structure determination. Topics include multidimensional NMR spectroscopy, including COSY, TOCSY and NOESY experiments, sequential assignments and structural analysis, practical methods and new developments in the field.  Recommended prerequisites:  Modern Methods in Structural Biology.

Overview of the basic principles governing protein structure and folding. Topics include stereochemical mechanisms by which protein secondary and tertiary structures are generated and stabilized, methods of prediction of tertiary structure from amino acid sequence, and the organization of folding motifs into protein structures. Instruction will be based on didactic material, discussion of the primary literature, and student projects utilizing computer graphics.

Introduction to the determination of crystal structures of biological macromolecules using X-ray crystallography, covering the following major topics:  properties of crystals and foundations of X-ray diffraction; the phase problem and methods for its solution including isomorphous replacement, molecular replacement, and multiwavelength anomalous dispersion; model building and model refinement; model analysis. Recommended prerequisites: Mathematical Methods or equivalent, Modern Methods in Structural Biology

Provides students with a basic understanding of enzyme mechanism and enzyme kinetic analysis.  Topics to be covered include basic Michaelis-Menten kinetics, multisubstrate reactions and inhibitor studies ranging from the methods to analyze simple competitive inhibitors to suicide or tight binding inhibitors.  These principles will be illustrated for a series of classic well-characterized enzyme reactions.  Emphasis is placed on quantitative analysis through a series of problem sets and through reading and discussion of the primary literature.

The operation of the nervous and muscular systems rests upon the activities of a constellation ion channels, which mediate electrical signaling by action potentials, intracellular communication by electrical and chemical synaptic transmission, transduction of sensory stimuli, and the excitation-contraction coupling. Drawing upon the techniques of biophysics, biochemistry, and molecular biology, students in this course will consider the structures and functions of representative channels.