Journal club

Journal club meetings are on Mondays at 5-6 pm in BCH 202.

June 11, 2018
DNA-RNA interactions are critical for chromosome condensation in Escherichia coli. - Copy

Qian, Z., Zhurkin, V. B., & Adhya, S. (2017). Proceedings of the National Academy of Sciences, 114(46), 12225-12230.

Abstract

PDF

presented by Maciej

June 11, 2018
Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

Narayanan, C. et al., Structure, 2018, 26 (3), p426-436.

PDF 

presented by Lim

May 7, 2018
Complete protein–protein association kinetics in atomic detail revealed by molecular dynamics simulations and Markov modelling

N. Plattner, S. Doerr, G. De Fabritiis, and F. Noe

Nature Chemistry volume 9, pages 10051011 (2017)

Abstract / PDF

presented by Nawrocki

May 7, 2018
Free Energy Calculations of Membrane Permeation: Challenges Due to Strong Headgroup–Solute Interactions

N. Pokhrel and L. Maibaum.
J. Chem. Theory Comput., 2018, 14, 1762-1771

Abstract / PDF

presented by Bercem

April 30, 2018
Protein homology model refinement by large-scale energy optimization

Park, H., Ovchinnikov, S., Kim, D. E., DiMaio, F., and Baker, D., Proc. Natl. Acad. Sci, USA, 2018, 115 (12) 3054-3059.

PDF 

presented by Lim

April 23, 2018
Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins

Lioy, Virginia S., et al. "Multiscale Structuring of the E. coli Chromosome by Nucleoid-Associated and Condensin Proteins." Cell (2018).

PDF / abstract

Presented by Maciej

April 23, 2018
Highly Disordered Amyloid-beta Monomer Probed by Single-Molecule FRET and MD Simulation

F. Meng, M.M.J. Bellaiche, J-Y. Kim, G.H. Zerze, R. Best, H.S. Chung, Biophysical Journal, 2018, 114, 870-884

Abstract | PDF

presented by Jaie

March 26, 2018
Trigger loop of RNA polymerase is a positional, not acid–base, catalyst for both transcription and proofreading

T. V. Mishanina, M. Z. Palo, D. Nayak, R. A. Mooney and R. Landick.
PNAS, 2017, 114, .

Abstract / PDF

presented by Bercem

March 26, 2018
Peptide Solubility Limits: Backbone and Side-Chain Interactions

Rahul Sarma, Ka-Yiu Wong, Gillian C. Lynch, and B. Montgomery Pettitt

J. Phys. Chem. B 2018.

Abstract / PDF

presented by Nawrocki

March 5, 2018
RNA force field with accuracy comparable to state-of-the-art protein force fields

Tan, Dazhi, et al. "RNA force field with accuracy comparable to state-of-the-art protein force fields." Proceedings of the National Academy of Sciences(2018): 201713027.

PDF / abstract

Presented by Maciej

 

March 5, 2018
Rational design of proteins that exchange on functional timescales

Davey, J. A., Damry, A. M., Goto, N. K., and Chica, R. A., Nat. Chem. Biol., 2017, 13, 1280-1285.

Abstract / PDF 

presented by Lim

February 26, 2018
Development of a Coarse-Grained Model of Collagen-Like Peptide (CLP) for Studies of CLP Triple Helix Melting

J.E. Condon, A. Jayaraman, J. Phys. Chem. B, 2018, 122, 1929-1939

Abstract / PDF

presented by Jaie

February 12, 2018
Liquid–Liquid Phase Separation in Oligomeric Peptide Solutions

Y. Wang, A. Lomakin, S. Kanai, R. Alex, and G. Benedek

Langumir 2017, 33,7715-7721.

Abstract / PDF

presented by Nawrocki

February 12, 2018
Balancing Force Field Protein−Lipid Interactions To Capture Transmembrane Helix−Helix Association

J. Domanski, M.S.P. Sansom, P. J. Stansfeld and R. B. Best
Journal of Chemical Theory and Computation, DOI:10.1021/acs.jctc.7b00983

Abstract / PDF

presented by Bercem

February 5, 2018
Kinetics from replica exchange molecular dynamics simulations

Stelzl, Lukas S., and Gerhard Hummer. 

Journal of chemical theory and computation 13.8 (2017): 3927-3935.

Abstract / PDF 

Presented by Maciej

February 5, 2018
Protein structure modeling and refinement by global optimization in CASP12

Hong SH, Joung I, Flores-Canales JC, Manavalan B, Cheng Q, Heo S, et al., Proteins: Structure, Function and Bioinformatics, in press.

Abstract / PDF 

presented by Lim

January 29, 2018
Long-timescale dynamics of the Drew-Dickerson dodecamer

2016 May 19;44(9):4052-66

 
 
presented by Charlie

January 29, 2018
Partially native intermediates mediate misfolding of SOD1 in single-molecule folding trajectories

S. S. Mojumdar et al., Nature Communications (2017), 8, 1881

Abstract / PDF

presented by Jaie

January 22, 2018
Quinary Interactions Weaken the Electric Field Generated by Protein Side-Chain Charges in the Cell-like Environment

N. Zhang, L An, J. Li, Z. Liu, and L. Yao

J. Am. Chem. Soc. 2017, 139,647-654.

Abstract / PDF

presented by Nawrocki

January 22, 2018
Composition Fluctuations in Lipid Bilayers

S. Baoukina, D. Rozmanov and D. P. Tieleman
Biophysical Journal (2018), 113, 2750-2761

Abstract / PDF

presented by Bercem