Recommended Readings: Tom Muir, Ph.D. Friday January 25, 2019

Friday Lectures

Friday, January 25, 2019  3:45 p.m

Caspary Auditorium

Tom Muir Ph.D.

Professor of Chemistry and Chair

Department of Chemistry

Princeton University

Painting Chromatin with Synthetic Protein Chemistry


Recommended Readings:

Empirical Articles

Nacev, B.A., Feng, L., Bagert, J.D. Lemiesz, A., et al. (2019). The expanding landscape of ‘oncohistone’ mutations in human cancers. NATURE, in press

Wojcik, Felix; Dann, Geoffrey P.; Beh, Leslie Y.; et al. (2018). Functional crosstalk between histone H2B ubiquitylation and H2A modifications and variants. NATURE COMMUNICATIONS. 9

Lu, Chao; Jain, Siddhant U.; Hoelper, Dominik; et al. (2016). Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. SCIENCE. 352 (6287): 844-849

Nguyen, Uyen T. T.; Bittoval, Lenka; Mueller, Manuel M.; et al. (2014). Accelerated chromatin biochemistry using DNA-barcoded nucteosome libraries. NATURE METHODS. 11 (8): 834-840

Fierz, Beat; Kilic, Sinan; Hieb, Aaron R.; et al. (2012). Stability of Nucleosomes Containing Homogenously Ubiquitylated H2A and H2B Prepared Using Semisynthesis. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 134 (48): 19548-19551

Review Paper

David, Yael; Muir, Tom W. (2017). Emerging Chemistry Strategies for Engineering Native Chromatin. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. 139 (27): 9090-9096

Mueller, Manuel M.; Muir, Tom W. (2015). Histones: At the Crossroads of Peptide and Protein Chemistry. CHEMICAL REVIEWS. 115 (6): 2296-2349

Chatterjee, Champak; Muir, Tom W. (2010). Chemical Approaches for Studying Histone Modifications. JOURNAL OF BIOLOGICAL CHEMISTRY. 285 (15): 11045-11050

Book Chapter

Holt, Matthew; Muir, Tom (2015). Application of the Protein Semisynthesis Strategy to the Generation of Modified Chromatin. ANNUAL REVIEW OF BIOCHEMISTRY. 84: 265-290

McGinty, Robert K.; Chatterjee, Champak; Muir, Tom W. (2009). Semisynthesis of Ubiquitylated Proteins. METHODS IN ENZYMOLOGY: NON-NATURAL AMINO ACIDS. 462: 225-243

Recommended Readings: Jue Chen, Ph.D., February 27

Friday Lecture Series / Ph.D. Recruitment Lecture
Friday, February 25, 2015
3:45 p.m., Caspary Auditorium

Jue Chen, Ph.D.,
Head of Laboratory of Membrane Biology and Biophysics,
The Rockefeller University
Investigator, Howard Hughes Medical Institute

Understanding Molecular Pumps: Insights from Structural BiologyRecommended Readings

Empirical Articles

Chen, S., Oldham, M. L., Davidson, A. L., & Chen, J. (2013). Carbon catabolite repression of the maltose transporter revealed by X-ray crystallography. Nature, 499(7458), 364-368. doi:10.1038/nature12232

Jin, M. S., Oldham, M. L., Zhang, Q., & Chen, J. (2012). Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans. Nature. 490(7421), 566-569. doi:10.1038/nature11448

Oldham, M. L., Chen, S., & Chen, J. (2013). Structural basis for substrate specificity in the Escherichia coli maltose transport system. Proceedings of the National Academy of Sciences, 110(45), 18132-18137. doi:10.1073/pnas.1311407110

Review Papers

Chen, J. (2013). Molecular mechanism of the Escherichia coli maltose transporterCurrent Opinion in Structural Biology, 23(4), 492-498. doi: 10.1016/

Faster Than Light?

Roll over Einstein: Law of physics challenged

By FRANK JORDANS, Associated Press – Sep 22, 2011 

GENEVA (AP) — One of the very pillars of physics and Einstein’s theory of relativity — that nothing can go faster than the speed of light — was rocked Thursday by new findings from one of the world’s foremost laboratories.

European researchers said they clocked an oddball type of subatomic particle called a neutrino going faster than the 186,282 miles per second that has long been considered the cosmic speed limit.    Read more about this experiment in NATURE.

NASA’s Gravity Probe B Confirms Two Einstein Space-Time Theories

NASA’s Gravity Probe B (GP-B) mission has confirmed two key predictions derived from Albert Einstein’s general theory of relativity, which the spacecraft was designed to test.  

The experiment, launched in 2004, used four ultra-precise gyroscopes to measure the hypothesized geodetic effect, the warping of space and time around a gravitational body, and frame-dragging, the amount a spinning object pulls space and time with it as it rotates.

GP-B determined both effects with unprecedented precision by pointing at a single star, IM Pegasi, while in a polar orbit around Earth. If gravity did not affect space and time, GP-B’s gyroscopes would point in the same direction forever while in orbit. But in confirmation of Einstein’s theories, the gyroscopes experienced measurable, minute changes in the direction of their spin, while Earth’s gravity pulled at them.

The findings are online in the journal Physical Review Letters.

Anomaly at U.S. Particle Accelerator: Evidence of Higgs Boson?

Tevatron; photo courtesy FermilabApril 8, 2011 – Fermi National Accelerator Laboratory physicists announced the discovery of a “bump” in data that, if verified, could signify the existence of a new particle or force of nature — or even be evidence of an unexpected form of the hypothetical Higgs boson particle. The finding stems from one of two experiments conducted at Fermi’s Tevatron, which collides beams of protons and antiprotons moving at energies of nearly 1 trillion electron volts. If the other experiment finds the same data bump, the result could be the most significant physics discovery in decades.

Recommended Readings: Marcelo O Magnasco PhD Jan 24, 2011

Monday Lecture Series

The Architecture of Biological Transport Networks

Marcelo O. Magnasco PhD

 Laboratory of Mathematical Physics

January24, 2011

4:00 p.m.-5:00 p.m. Caspary Auditorium


Recommended Readings:
Roth-Nebelsick A, Uhl D, Mosbrugger V, Kerp H.  2001. Evolution and function of leaf venation architecture: A review.  ANNALS OF BOTANY   87(5):553-566

Katifori E. Szollosi GJ, Magnasco MO.  2010.  Damage and fluctuations induce loops in optimal transport networksPHYSICAL REVIEW LETTERS   104(4): article number 048704  

Corson, F.  2010.  Fluctuations and redundancy in optimal transport networks  Physical  Review  Letters.  104(4):048703

Sack L,  Dietrich EM, Streeter CM, Sanchez-Gomez D, Holbrook NM.  2008,  Leaf palmate venation and vascular redundancy confer  tolerance of hydraulic disruption.  PNAS  105(5):1567-1572

Laguna MF.  2008. The role of elastic stresses on leaf venation morphogenesis. PLOS COMPUTATIONAL BIOLOGY  4 :e1000055 2008

Xia QL.  2007.  The formation of a tree leafEASIM-Control Optimisation and Calculus of Variations.  13(2):359-377

Bohn S, Magnasco MO.  2007.   Structure, scaling, and phase transition in the optimal transport network.  PHYSICAL REVIEW LETTERS   98(8): Article Number: 088702   

Durand M.  2006.  Architecture of optimal transport networks.  PHYSICAL REVIEW E  73: 0161116

Nelson T.  1997.  Leaf  vascular pattern  formation.  PLANT CELL   9:1121   Request from Markus Library, x 8916

The Birth of Time

Physicists from the Faculty of Physics, University of Warsaw have put forward — on the pages of Physical Review D — a new theoretical model of quantum gravity describing the emergence of space-time from the structures of quantum theory. It is not only one of the few models describing the full general theory of relativity advanced by Einstein, but it is also completely mathematically consistent. “The solutions applied allow to trace the evolution of the Universe in a more physically acceptable manner than in the case of previous cosmological models,” explains Prof. Jerzy Lewandowski from the Faculty of Physics, University of Warsaw (FUW).

New Theoretical Model for Moving Polymers Through Membranes

Moving Polymers Through Pores

ScienceDaily (July 13, 2010) — The movement of long chain polymers through nanopores is a key part of many biological processes, including the transport of RNA, DNA, and proteins. New research reported in The Journal of Chemical Physics, which is published by the American Institute of Physics, describes an improved theoretical model for this type of motion. 

The new model addresses both cylindrical pores and tapering pores that simulate the α-hemolysin membrane channel. “Current models do not take into account the motion of the polymer inside the pore,” says author Anatoly Kolomeisky of Rice University. “The leading monomer can move back and forth many times before it finally crosses the line to the other side of the membrane. Not accounting for this behavior introduces errors into predictions.”

Recommended Readings: Konstantin Goulianos Ph.D. May 24 2010

Monday Seminar Series

Rockefeller at the Large Hadron C ollider

Konstantin Goulianos, Ph.D.,


Laboratory of Experimental High Energy Physics

The Rockefeller University

May 24, 2010

3:45 p.m.-5:00 p.m.  Welch Hall Level Two


Recommended Readings:

 The CMS Collaboration. 2010. Measurement of Bose–Einstein Correlations in  proton-proton  Collisions at p s =0.9 and 2.36 TeV at the LHC.  CERN-PH-EP-2010-010 2010/05/19

The CMS Collaboration. 2010. Transverse-momentum and pseudorapidity distributions of  charged hadrons in pp collisions at ps = 7 TeV.  CERN-PH-EP-2010-009 2010/05/19

Chatrchyan, S., et al. incl.  Bhatti, A., Demortier, L., Goulianos,  K., Hatakeyama, K.,  Mesropian, C.   2009  The CMS experiment at the CERN LHC. JOURNAL OF  INSTRUMENTATION    3( S08004).

Merali, Zeenya.  2010.  Physics: The Large Human Collider  Nature 464: 482-484    doi:10.1038/464482a

Brumfield, Geoff.  2009.  LHC sees particles circulate once more Nature News (23 November  2009) doi:10.1038/news.2009.1104

 The CMS Collaboration.  (2010). Transverse-momentum and pseudorapidity distributions of charged hadrons in pp   collisions at root s=0.9 and 2.36 TeV.  JOURNAL OF HIGH ENERGY PHYSICS    issue 2 (041).

Abulencia, A., Adelman, J., Affolder, T., et al.  2007.  Observation of exclusive electron- postitron Production in hadron-handron.   Physical Review Letters   98(11  article number 112001)

Goulianos K .  2005.  Multigap diffraction at LHC . 2005.  Conference Information: 13th  International Workshop on Deep Inelastic Scattering (DIS 2005), APR 27-MAY 01,  2005 Madison, WI.  Deep Inelastic Scattering.   AIP CONFERENCE  PROCEEDINGS   792: 515-518