Syllabus of Lectures - 2008

Date Topic Lecture Lecturer
T, 22 Jan 2008 Course introduction and overview of genomics & proteomics
Required Reading:
- DNA sequencing: bench to bedside and beyond

GTM-
GTM+SA
SA-
F, 25 Jan 2008 Principles of thermodynamics and kinetics
Required Reading: Lehninger, Principles of Biochemistry,  pp 47-58 
GTM
T, 29 Jan 2008 Conformational properties of proteins
Required Reading:
- B&H, Chapters 1 and 2, Intro to Structural Bioinformatics
GTM
F, 1 Feb 2008 Tools of bioinformatics: Blast, PsiBlast, DNA sequence databases
Required Reading:
-
A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins
pdf document GTM
T, 5 Feb 2008 Protein sequence and structure databases
Required Reading:
- Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs
pdf document GTM
F, 8 Feb 2008 Protein domains and folds: SCOP, CATH, DALI
Required Reading:
- A global representation of the protein fold space
- Hiddden Markov Models
pdf document GTM
T, 12 Feb 2008 New strategies and technologies for DNA sequencing
Required Reading:
- The Race to Read Genomes on a Shoestring, Relatively Speaking
- Whole-genomere-sequencing
- Genome sequencing in micro fabricated high-density picolitre reactors
- Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing
- Massively parallel sequencing
pdf document Part Ia
pdf document Part Ib
pdf document Part II
SA
F, 15 Feb 2008 Analytical protein chemistry
Required Reading: none
pdf document SA
T, 19 Feb 2008 Preparative protein chemistry
Required Reading:
- Protein Purification
- Protein Purification Handbook, pages 9-27 and 61-71.
pdf document SA
F, 22 Feb 2008 SNOW DAY SA
T, 26 Feb 2008 Protein mass spectrometry
Required Reading:
- Biological Mass Spectrometry: A Primer, pp. 415 - 419 only
- Analysis of Proteins and Proteomes by Mass Spectrometry, pp. 438 - 447 only
- The biological impact of mass-spectrometry-based proteomics
Take-home Exam I handed out
pdf document SA
F, 29 Feb 2008 Protein folding in vitro
Required Reading:
- Folding and binding: implementing the game plan
- The protein folding problem: when will it be solved?
- Protein Folding and Unfolding at Atomic Resolution
- Proteins: Structures and Molacular Principles
Suggested Reading:
- Progress in Modeling of Protein Structures and Interactions
pdf document SA
T, 4 Mar 2008 Protein folding in vivo
Required Reading:
- Experimental investigation of protein folding and misfolding
-
Protein degradation and protection against misfolded or damaged proteins
Suggested Reading:
-
Pathways of chaperone-mediated protein folding in the cytosol
pdf document SA
F, 7 Mar 2008 Protein X-ray crystallography
Take-home Exam I due
Required Reading:
- Protein Crystallography for non-crystallographers
pdf document GTM/RG
T, 11 Mar 2008 Protein-protein interactions I
Required Reading:
-
Interactions with Other Molecules
-
Binding in the growth hormone receptor complex
- The molecular architecture of protein–protein binding sites
Suggested Reading:
-
Additivity-based prediction of equilibrium constants for some protein-protein associations
pdf document SA
F, 14 Mar 2008 NMR Principles
Required Reading:
- Structural Bioinformatics Chapter 5: Macromolecular Structure Determination by NMR Spectroscopy
pdf document GTM
T, 18 Mar 2008 Spring Break
   
F, 21 Mar 2008
Spring Break    
T, 25 Mar 2008 Protein NMR Structure Analysis
Suggested Reading:
- Protein NMR Spectroscopy Chapter 10: Sequential Assignment, Structure Determination
pdf document GTM
F, 28 Mar 2008 Protein-protein interactions II
Required Reading:
-
Reaching for high-hanging fruit in drug discovery at protein–protein interfaces
pdf document SA
T, 1 Apr 2008 DNA microarrays
Required Reading:
- The Affymetrix GeneChip® Platform: An Overview
- Microarray technology: beyond transcript profiling and genotype analysis
Take-home Exam II handed out
Papers for student presentations chosen. Select a paper from the Research Paper Presentations list to present.
pdf document SA
F, 4 Apr 2008 Reading:
- Biochemistry, Chapter 4: Enzymes: Biological Catalysts
   
T, 8 Apr 2008 RNA interference
Required Reading:
- RNA Silencing Poster
- RNA Interference: Big Applause for Silencing in Stockholm
- DNA Study Forces Rethink of What It Means to Be a Gene
- Encyclopaedia of humble DNA
- Genome project turns up evolutionary surprises
pdf document SA
F, 11 Apr 2008 Predicting function from structure, disorder prediction, GRASP, CONSURF
Required Reading:
- Structural genomics: keystone for a Human Proteome Project
- Protein Structure Initiative: Phase 3 or Phase Out
Take-home Exam II due
pdf document GTM/JH
T, 15 Apr 2008 LABORATORY TOURS
  GTM
F, 18 Apr 2008 Student Presentations:
Rachel Belote, Paper 1
Irina Fridman, Paper 10
  GTM+SA
T, 22 Apr 2008 Student Presentations:
Petrit Mavraj, Paper 20
Kaitlyn Turo, Paper 19
Paul Harvilla, Paper 7
  GTM+SA
F, 25 Apr 2008
Student Presentations:
Daya Patel, Paper 9
Mai Mahmoud, Paper 8
Michael Merolla, Paper 2
  GTM+SA
T, 29 Apr 2008
Student Presentations:
Joanne Ahn, Paper 13
Ria John, Paper 16
Rabab Haider, Paper 12
  GTM+SA
F, 2 May 2008 Student Presentations:
Seema Sahdev, Paper 23
Zach Perlman, Paper 15
William Buchwald, Paper 5
Take-home Exam III handed out
  GTM+SA
MONDAY, MAY 12 Take Home Exam III Due   GTM+SA
Sample Presentations from 2004:
  • Kate Drahos, HTP Protein-Protein Interaction Analysis [HTML] [PPT]
  • Dan Kulp, Macromolecular Complexes [HTML] [PPT]
Each take-home exam will count for 30% of your grade.

The Student Presentations + Exam III will count for 40% of your grade. There will be no final exam.

Prof. Montelione’s email address: guy@cabm.rutgers.edu
Prof. Anderson’s email address: anderson@cabm.rutgers.edu