Journal club

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

October 2, 2017
Role of Hydration Layer in Dynamical Transition in Proteins: Insights from Translational Self-Diffusivity

Prithwish K. Nandi and Niall J. English

J. Phys. Chem. B, 2016, 120 (47), pp 12031–12039

Abstract / PDF

presented by Nawrocki

October 2, 2017
Dynamics of bridge helix bending in RNA polymerase II

Z-F. Wang, Y-B. Fu, P-Y. Wang and P. Xie
Proteins (2017), 85, 614–629

Abstract / PDF

presented by Bercem

September 25, 2017
Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Trussart M, Yus E, Martinez S, et al.

Nature Communications. 2017;8:14665. doi:10.1038/ncomms14665.

Abstract / PDF

 

Presented by Maciej

 

September 25, 2017
Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau

S. Ambadipudi, J. Biernat, D. Riedel, E. Mandelkow, M. Zweckstetter

Nature Communications (2017), 8, 275.

Abstract / PDF

presented by Jaie

July 17, 2017
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome

W. C. Hacker, S. Li, A. H. Elcock, NAR Breakthrough Article, 2017.

Abstract / PDF

presented by Asli

July 17, 2017
Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics

Galvelis, R. and Sugita, Y., ​J. Chem. Theory Comput., 2017, 13 (6), pp 2489–2500.

Abstract / PDF 

presented by Lim

July 10, 2017
Crowding-Controlled Cluster Size in Concentrated Aqueous Protein Solutions: Structure, Self- and Collective Diffusion

M. K. Braun, M. Grimaldo, F. Roosen-Runge, I. Hoffmann, O. Czakkel, M. Sztucki, F. Zhang, F. Schreiber, T. Seydel

J. Phys. Chem. Lett., 2017, 8 (12), pp 2590–2596

Abstract / PDF

presented by Nawrocki

July 10, 2017
New Continuum Approaches for Determining Protein-Induced Membrane Deformations

D. Argudo, N. P. Bethel, F. V. Marcoline, C. W. Wolgemuth and M. Grabe
Biophysical Journal (2017), 112, 2159-2172

Abstract / PDF

presented by Bercem

May 1, 2017
FISH-ing for captured contacts: towards reconciling FISH and 3C

G. Fudenberg, M. Imakaev, bioRxiv (2016).

Abstract / PDF

presented by Asli

April 24, 2017
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

Justin A. Lemkul  and Alexander D. MacKerell Jr.

J. Chem. Theory Comput., Article ASAP

Abstract / PDF

 

Presented by Maciej

 

April 24, 2017
Building a More Predictive Protein Force Field: A Systematic and Reproducible Route to AMBER-FB15

Wang, L.-P., McKiernan, K.A., Gomes, J., Beauchamp, K.A., Head-Gordon, T., Rice, J.E., Swope, W.C., Martinez, T.J., and Pande, V.S.

J. Phys. Chem. B, Article ASAP​

Abstract / PDF 

presented by Lim

April 17, 2017
Role of Molecular Flexibility and Colloidal Descriptions of Proteins in Crowded Environments from Small-Angle Scattering

Maria Monica Castellanos, Nicholas J. Clark, Max C. Watson, Susan Krueger, Arnold McAuley, and Joseph E. Curtis

J. Phys. Chem. B, 2016, 120 (49), pp 12511–12518

Abstract / PDF

presented by Nawrocki

April 17, 2017
Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP

J. K. Leman, S.Lyskov and R. Bonneau
BMC Bioinformatics (2017), 18, 115

Abstract / PDF

presented by Bercem

April 10, 2017
Direct Comparison of Amino Acid and Salt Interactions with Double-Standed and Single-Stranded DNA from Explicit-Solvent Molecular Dynamics Simulations

C. T. Andrews, B. A. Campbell and A. H. Elcock, J. Chem. Theory Comput. (2017), ASAP 

Abstract / PDF

presented by Asli

March 20, 2017
Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics

Aytenfisu AH, Spasic A, Grossfield A, Stern HA, Mathews DH.

J Chem Theory Comput. 2017 Feb 14;13(2):900-915.

Abstract / PDF

Missing figure

presented by Maciej

March 20, 2017
Modeling Protein Conformational Transition Pathways Using Collective Motions and the LASSO Method

T. W. Hayes and I. H. Moal

Journal of Chemical Theory and Computation (2017), 13 (3), 1401-1410.

Abstract / PDF 

presented by Lim

 

March 13, 2017
Structure–Kinetic Relationships of Passive Membrane Permeation from Multiscale Modeling

C. L. Dickson, V. Hornak, R. A. Pearlstein and J. S. Duca
Journal of the American Chemical Society (2017), 139, 442-452

Abstract / PDF

presented by Bercem

March 13, 2017
Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation

N. Salvi, A. Abyzov, and M. Blackledge

J. Phys. Chem. Lett. (2016), 7, 2483-2489

Abstract / PDF

presented by Nawrocki

February 6, 2017
Compaction and segregation of sister chromatids via active loop extrusion

A. Goloborodko, M. V. Imakaev, J. F. Marko and L. Mirny, eLife (2016), 5, e14864.

Abstract / PDF

presented by Asli

January 30, 2017
The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential

J. Lee, K. Joo, B. R. Brooks, and J. Lee

Journal of Chemical Theory and Computation (2015), 11, 3211.

Abstract / PDF 

presented by Lim