Department of Biochemistry
School of Medicine & Biomedical Sciences
BCH 507 Protein Structure & Function
Spring Semester, 2009
Credits: Variable, 2-3
Farber 134B, Tuesdays, 10:30-12:30 PM

 Course Coordinator:  Daniel Kosman (829-2842; camkos@buffalo.edu)
Instructors: D. Kosman, Jennifer Surtees, Mark Sutton, Kenneth Blumenthal

Click here for a [PDF] of the Course Schedule.

Click here for the [PDF] "Exploring the Energy Landscape of Protein Structure and Function"

Click here for a [Link]  to Dr. Kosman's Teaching Home Page for additional information.
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Part 1: AFM of DNA Structure & Protein-DNA Interactions: Dr. Jennifer Surtees

Here's a link for some AFM background.  Note: the papers that we will discuss will use the "tapping" mode of AFM, so take and remind yourself of what that means:
http://spm.phy.bris.ac.uk/techniques/AFM/

Here are the AFM papers that we will discuss:

Marilley et al (2007)
Wacker et al (2007)

Part 2: TIRFM for Dynamic Protein-DNA Interactions: Dr. Jennifer Surtees

TIRFM for dynamic protein-DNA interactions.

Here are some links for information on TIRFM (total internal reflection fluorescence microscopy):
http://motility.york.ac.uk/poster/tirfm.shtml

http://www.feinberg.northwestern.edu/cif/tirf.htm

http://www.microscopyu.com/articles/fluorescence/tirf/tirfintro.html

Here are the TIRFM papers that we will discuss:

Graneli et al (2006)
Gorman et al (2007)

Powerpoint Presentation of 1/29 lecture.

Part 3: "Optical Tweezers" to Characterize Protein Interactions with DNA: Dr. Jennifer Surtees

Here is a link for some background information:
http://www.stanford.edu/group/blocklab/Optical%20Tweezers%20Introduction.htm

Here is a review paper:
Block (1992)

And if you're really interested, another review paper:
Kimura and Bianco (2006)

Here are two primary papers that use optical tweezers in very different ways:
Jiang et al (2005)
Spies et al (2003)

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 Ion Channel Structure and Function:  Dr. Blumenthal

Course Information [PDF]
Lecture Slides [PPT] 

Links to Readings:

Review Articles and Commentaries:
Catterall, WA (2000) Neuron 26, 13-25. [PDF]
 
Research Articles:
Doyle, MacKinnon et al (1998) Science 280, 69-77 [PDF]
Yang and Horn (1995) Neuron 15, 213. [PDF]
Jiang, MacKinnon et al (2003) Nature 423, 33-41. [PDF]
Jiang, MacKinnon et al (2003) Nature 423, 42-48. [PDF]
Long et al (2005) Science 309, 897. [PDF]
Long et al (2005) Science 309, 903. [PDF]
Laine et al (2003) Neuron 39, 467. [PDF]
Starace and Bezanilla (2004) Nature 427, 548. [PDF]
Posson et al (2005) Nature 436, 848. [PDF]
Chanda et al (2005) Nature 436, 852. [PDF]
Schmidt et al (2006) Nature 444, 775. [PDF]
Campos et al (2007) PNAS 104, 7904 [PDF]

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