Yan Xu 

Research efforts in Dr. Xu's group are directed to three projects: (1); membrane protein structures and dynamics by NMR; (2); low-affinity drug interaction with membrane proteins, and (3); gene and stem cell therapy for brain protection and revitalization after cardiac arrest and resuscitation. The current focuses are as follows. For Project 1, NMR is used to determine the transmembrane domain structures of the human glycine receptor, which is the primary inhibitory receptors in the spinal cord and responsible for a wide range of diseases. The long-term goal is to provide the structural basis for novel design of drugs that are disease specific and devoid of side effects. For Project 2, experimental and theoretical approaches are combined to study how low affinity neurological agents, such as alcohol and general anesthetics, exert their effects on the central nervous system at the molecular level. The goal is to shed new lights on the great unsolved mystery of modern medicine: the molecular mechanisms of general anesthesia. For Project 3, new gene therapy strategies are being developed to target a special event called reperfusion injury after cardiac arrest and resuscitation. Recently, Dr. Xu's group combines gene therapy with stem cell therapy using a non-controversial source of stem cells, in an effort to stop and reverse the neuronal loss and to rebuild neuronal circuitry after reperfusion from prolonged cardiac arrest or stroke.
Students in Dr. Xu's laboratory have the opportunity to learn a variety of modern techniques, including expression and purification of membrane proteins, immunohistochemistry, high-resolution nuclear magnetic resonance imaging and spectroscopy, imaging reconstruction, 3-D protein structure calculation, and molecular dynamics simulations.


Department of Anesthesiology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3, Room 2048
3501 Fifth Avenue
Pittsburgh, PA 15260

P 412- 648-9922
F 412-648-8998
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Date PS Reading Lecture Notes Instructor Topic
Aug 25 (M)   1.pdf 2.pdf   Lanni QM I
Aug 27 (W)   1.pdf   Lanni QM II
Aug 29 (F)   1.pdf   Lanni UV absorption
Sep 1 (M)       Labor Day  
Sep 3 (W)   1.pdf   Lanni Fluorescence I
Sep 5 (F)   1.pdf   Lanni Fluorescence II
Sep 8 (M)       Asher Circular Dichroism I
Sep 10 (W)       Asher Circular Dichroism II
Sep 12 (F)       Asher IR/Raman
Sep 15 (M)       Furey Intro Proteins, Exam I (QM-IR/Raman)
Sep 17 (W)   1.pdf 2.pdf   Ishima NMR I
Sep 19 (F)       Ishima NMR II
Sep 22 (M)       Ishima NMR III
Sep 24 (W)       Ishima NMR IV
Sep 26 (F)       Ishima NMR V
Sep 29 (M)       Ishima NMR VI
Oct 1 (W)       Ishima NMR VII
Oct 3 (F)       Ishima NMR vs other spectroscopies
Oct 6 (M)   1.pdf   van der Wel Solid State NMR I
Oct 8 (W)       van der Wel Solid State NMR II
Oct 10 (F)       van der Wel ESR
Oct 13 (M)       Leuba Single molecule I
Oct 15 (W)       Leuba Single molecule II
Oct 17 (F)       CMU Fall Break  
Oct 20 M)       Van Houten Protein-DNA Interactions I
Oct 22 (W)       Van Houten Protein-DNA Interactions II
Oct 24 (F)       Ishima Exam II (NMR-ESR)
Oct 27 (M)          
Oct 29 (W)       BGSA Symposiun  
Oct 30 (Th)       Evilevitch Calorimitry
Oct 31 (F)       Furey X-ray I
Nov 3 (M)       Furey X-ray II
Nov 5 (W)       Furey X-ray III
Nov 7 (F)       Furey X-ray IV
Nov 10 (M)       Furey X-ray V
Nov 12 (W)       Furey X-ray VI
Nov 14 (F)       Furey X-ray VII
Nov 17 (M)       Furey X-ray VIII
Nov 19 (W)       Furey Exam III (Single molecule -Xray)
Nov 21 (F)     1.pdf Conway Electron Microscopy I
Nov 24 (M)     1.pdf Conway Electron Microscopy II
Nov 26 (W)       Thanksgiving  
Nov 28 (F)       Thanksgiving  
Dec 1 (M)     1.pdf Conway Electron Microscopy III
Dec 3 (W)     1.pdf Yates Mass Spec I
Dec 5 (F)     1.pdf Yates Mass Spec II
Dec 8 (M)          
Dec 17 (W)          
Dec 18 (Th)          

Molecular Biophysics I
11:10-12:20 / BST3 1018

Molecular Biophysics I (MOLBPH2001 University of Pittsburgh)
Structural Biophysics (03-871 Carnegie Mellon University)
Location and Time: BST3 Room 1018 (University of Pittsburgh). 11:10 -12:20 MWF.

Course Website: http://www.structbio.pitt.edu/main/sbl2014 

Current schedule, links to lecture handouts, powerpoint slides, assigned readings, problem sets, and other online material can be found here.

Course Description: The physical properties of biological macromolecules and the methods used to analyze their structure and function are discussed. Topics covered include: protein architecture and folding; nucleic acid structures and energetics; structure determination by X-ray crystallography and NMR; biological spectroscopy with emphasis on absorption, fluorescence, electron spin resonance and NMR spectroscopies; other methods to characterize proteins and protein-ligand interactions, such as mass spectrometry, calorimetry, surface plasmon resonance, and single molecule fluorescence techniques.

The goal of the course is to provide sufficient theoretical background to allow the student to critically evaluate the current literature and to ascertain which techniques would be most appropriate to solve current research problems in the laboratory.

Prerequisites: Undergraduate biochemistry, physical chemistry, calculus.

Suggested prerequisite: Undergraduate quantum mechanics, linear/matrix algebra.

Recommended Textbook: Principles of Physical Biochemistry, 2nd Ed. (2005) K. van Holde, C. Johnson, and P. S. Ho.

Textbooks on Reserve in Mellon Inst. Library:

  • Introduction to Protein Structure Branden & Tooze. 
  • Structure and Mechanism in Protein Structure. Fersht 
  • Principles of Nucleic Acid Structure Saenger. 
  • Biophysical Chemistry I and II Cantor & Schimmel. 
  • Physical Biochemistry David Freifelder. 
  • Principals of Physical Biochemistry Van Holde et al. 
  • Spectroscopy for the biological sciences Hammes 
  • NMR of Proteins and Nucleic Acids Wüthrich. 
  • A complete introduction to modern NMR spectroscopy. Macomber 
  • NMR for physical and biological scientists. Pochapski 
  • Crystallography Made Crystal Clear Rhodes. 
  • Crystal structure analysis for chemists and biologists. Glusker 
  • Outline of crystallography for biologists. Blow 
  • Principles of Fluoresence Spectroscopy Lakowicz. 

Instructors: Appointments with instructors can be made by contacting them by email:

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Peijun Zhang

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Bill Furey

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Patrick van der Wel

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Fred Lanni

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Nathan Yates

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Rieko Ishima

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Ben Van Houten

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Sanford Leuba

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Alex Evilevitch

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Sanford Asher
 

 

  

 

Homework: Approximately 5 problem sets will be assigned during the course, and they will be graded. Some of these will be based on readings from the primary literature.

Exams & Final: There will be at least three one-hour exams, either during the class period or take home. They weigh heavily in the final grade, but 
assignments also contribute significantly.

Lecture notes, reading, and homework available here.

Software tools and links here.

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Course Schedule

Date Instructor Topic Notes
Aug 25 (M) Lanni QM I CMU/Pitt Classes start
Aug 27 (W) Lanni QM II  
Aug 29 (F) Lanni UV absorption  
Sep 1 (M) Labor Day   No class
Sep 3 (W) Lanni Fluorescence I  
Sep 5 (F) Lanni Fluorescence II  
Sep 8 (M) Asher Circular Dichroism I Rm 706, Chevron Sc. Ctr.
Sep 10 (W) Asher Circular Dichroism II Rm 706, Chevron Sc. Ctr.
Sep 12 (F) Asher IR/Raman Rm 706, Chevron Sc. Ctr.
Sep 15 (M) Furey Intro Proteins, Exam I (QM-IR/Raman)  
Sep 17 (W) Ishima NMR I  
Sep 19 (F) Ishima NMR II  
Sep 22 (M) Ishima NMR III  
Sep 24 (W) Ishima NMR IV  
Sep 26 (F) Ishima NMR V  
Sep 29 (M) Ishima NMR VI  
Oct 1 (W) Ishima NMR VII  
Oct 3 (F) Ishima NMR vs other spectroscopies  
Oct 6 (M) van der Wel Solid State NMR I  
Oct 8 (W) van der Wel Solid State NMR II  
Oct 10 (F) van der Wel ESR  
Oct 13 (M) Leuba Single molecule I Pitt Fall Break (Ignore)
Oct 15 (W) Leuba Single molecule II  
Oct 17 (F) CMU Fall Break   No class
Oct 20 M) Van Houten Protein-DNA Interactions I  
Oct 22 (W) Van Houten Protein-DNA Interactions II  
Oct 24 (F) Ishima Exam II (NMR-ESR)  
Oct 27 (M)     moved to Oct 30, 3:00 PM
Oct 29 (W) BGSA Symposiun   No class
Oct 30 (Th) Evilevitch Calorimetry Note! 3:00 PM start
Oct 31 (F) Furey X-ray I  
Nov 3 (M) Furey X-ray II  
Nov 5 (W) Furey X-ray III  
Nov 7 (F) Furey X-ray IV  
Nov 10 (M) Furey X-ray V  
Nov 12 (W) Furey X-ray VI  
Nov 14 (F) Furey X-ray VII  
Nov 17 (M) Furey X-ray VIII  
Nov 19 (W) Furey Exam III (Single molecule -Xray)  
Nov 21 (F) Conway Electron Microscopy I  
Nov 24 (M) Conway Electron Microscopy II  
Nov 26 (W) Thanksgiving   No class
Nov 28 (F) Thanksgiving   No class
Dec 1 (M) Conway Electron Microscopy III  
Dec 3 (W) Yates Mass Spec I  
Dec 5 (F) Yates Mass Spec II  
Dec 8 (M)   CMU/Pitt Last Day
Dec 17 (W)   Pitt grades due
Dec 18 (Th)   CMU grades due

Schedule in PDF format available for download here.

 

Dean Duncan
Department Administrator

In-Ja Byeon, PhD
Scientist

Janet Zambotti
Assistant to the Chair

Teresa Brosenitsch, PhD
PCHPI Coordinator

    

Amy Farrell
Financial Administrator

Doug Bevan
Systems Administrator

Mike Delk
NMR Manager

Doowon Lee
X-ray Manager

    

Miranda Wimer
Purchaser

          
           
           
           

 

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