Ion Counting from Explicit-Solvent Simulations and 3D-RISM

Slides:



Advertisements
Similar presentations
Volume 111, Issue 10, Pages (November 2016)
Advertisements

Volume 107, Issue 9, Pages (November 2014)
Voltage-Dependent Hydration and Conduction Properties of the Hydrophobic Pore of the Mechanosensitive Channel of Small Conductance  Steven A. Spronk,
Volume 109, Issue 7, Pages (October 2015)
Volume 98, Issue 2, Pages (January 2010)
Peter J. Mulligan, Yi-Ju Chen, Rob Phillips, Andrew J. Spakowitz 
Steve P. Meisburger, Suzette A. Pabit, Lois Pollack 
Toshiro Oda, Keiichi Namba, Yuichiro Maéda  Biophysical Journal 
Olivier Fisette, Stéphane Gagné, Patrick Lagüe  Biophysical Journal 
Ion Permeation through a Narrow Channel: Using Gramicidin to Ascertain All-Atom Molecular Dynamics Potential of Mean Force Methodology and Biomolecular.
Jing Han, Kristyna Pluhackova, Tsjerk A. Wassenaar, Rainer A. Böckmann 
Structure and Dynamics of Calmodulin in Solution
Composition Fluctuations in Lipid Bilayers
Partially Assembled Nucleosome Structures at Atomic Detail
Marc Jendrny, Thijs J. Aartsma, Jürgen Köhler  Biophysical Journal 
A Computational Framework for Mechanical Response of Macromolecules: Application to the Salt Concentration Dependence of DNA Bendability  Liang Ma, Arun.
Volume 90, Issue 4, Pages (February 2006)
Robert M. Elder, Arthi Jayaraman  Biophysical Journal 
Effects of Hofmeister Ions on the α-Helical Structure of Proteins
Monika Sharma, Alexander V. Predeus, Nicholas Kovacs, Michael Feig 
Prediction of Thylakoid Lipid Binding Sites on Photosystem II
Yong Wang, Paul Penkul, Joshua N. Milstein  Biophysical Journal 
Steve P. Meisburger, Suzette A. Pabit, Lois Pollack 
Volume 107, Issue 3, Pages (August 2014)
Tests of Continuum Theories as Models of Ion Channels. II
Rainer A. Böckmann, Helmut Grubmüller  Biophysical Journal 
Volume 93, Issue 2, Pages (July 2007)
Dynamic Motions of the HIV-1 Frameshift Site RNA
Electrostatic Free Energy Landscapes for DNA Helix Bending
J.L. Robertson, L.G. Palmer, B. Roux  Biophysical Journal 
Yuno Lee, Philip A. Pincus, Changbong Hyeon  Biophysical Journal 
Volume 111, Issue 10, Pages (November 2016)
Volume 96, Issue 7, Pages (April 2009)
Volume 103, Issue 2, Pages (July 2012)
Calcium Enhances Binding of Aβ Monomer to DMPC Lipid Bilayer
Till Siebenmorgen, Martin Zacharias  Biophysical Journal 
Volume 102, Issue 9, Pages (May 2012)
Tests of Continuum Theories as Models of Ion Channels. I
Volume 92, Issue 1, Pages L07-L09 (January 2007)
Molecular Dynamics Study of the KcsA Potassium Channel
Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter- nucleosome Interaction  Ruihan Zhang, Jochen Erler, Jörg Langowski  Biophysical.
Grischa R. Meyer, Justin Gullingsrud, Klaus Schulten, Boris Martinac 
Volume 103, Issue 5, Pages (September 2012)
Volume 88, Issue 4, Pages (April 2005)
Chetan Poojari, Dequan Xiao, Victor S. Batista, Birgit Strodel 
Volume 107, Issue 9, Pages (November 2014)
Thomas H. Schmidt, Yahya Homsi, Thorsten Lang  Biophysical Journal 
Volume 111, Issue 1, Pages (July 2016)
On the Role of Acylation of Transmembrane Proteins
Volume 111, Issue 4, Pages (August 2016)
Open-State Models of a Potassium Channel
Volume 114, Issue 1, Pages (January 2018)
Ion-Induced Defect Permeation of Lipid Membranes
Robust Driving Forces for Transmembrane Helix Packing
Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels  Manami Nishizawa, Kazuhisa Nishizawa 
Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels  Manami Nishizawa, Kazuhisa Nishizawa 
Agnes Noy, Anthony Maxwell, Sarah A. Harris  Biophysical Journal 
Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a.
Partially Assembled Nucleosome Structures at Atomic Detail
Sebastian Fritsch, Ivaylo Ivanov, Hailong Wang, Xiaolin Cheng 
Chze Ling Wee, David Gavaghan, Mark S.P. Sansom  Biophysical Journal 
Shayantani Mukherjee, Sean M. Law, Michael Feig  Biophysical Journal 
Interactions of the Auxilin-1 PTEN-like Domain with Model Membranes Result in Nanoclustering of Phosphatidyl Inositol Phosphates  Antreas C. Kalli, Gareth.
Martini Coarse-Grained Force Field: Extension to RNA
Atomic Level Rendering of DNA-Drug Encounter
Volume 98, Issue 4, Pages (February 2010)
Distribution of Halothane in a Dipalmitoylphosphatidylcholine Bilayer from Molecular Dynamics Calculations  Laure Koubi, Mounir Tarek, Michael L. Klein,
Volume 98, Issue 3, Pages (February 2010)
Molecular Dynamics Simulation of a Synthetic Ion Channel
David L. Bostick, Karunesh Arora, Charles L. Brooks 
Presentation transcript:

Ion Counting from Explicit-Solvent Simulations and 3D-RISM George M. Giambaşu, Tyler Luchko, Daniel Herschlag, Darrin M. York, David A. Case  Biophysical Journal  Volume 106, Issue 4, Pages 883-894 (February 2014) DOI: 10.1016/j.bpj.2014.01.021 Copyright © 2014 Biophysical Society Terms and Conditions

Figure 1 Ion counting using the two-domain approach (46), adapted from Anderson and Record (56). The simulated system is separated into two regions, dark gray (region 1) and light gray (region 2), with the boundary between the two regions shown as a dashed line. Region 1 has to be chosen so that it contains at least all the solvent and cosolvent within the correlation radius (see text) from the DNA, and region 2 so that it resembles the bulk with uniform concentration of salt. Using this approach, a formula for the PIPs can be derived that depends on the salt bulk (region 2) concentration. This method may be useful when the g(r) cannot be easily defined. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 2 Cylindrical shells of sodium ion density around 24L DNA at 0.7452 M NaCl calculated by MD (upper row), 3D-RISM-PSE-4 (middle row), and NLPB (lower row). The shells isolate density extending radially from the DNA center of mass for 0–5 Å (left), 5–7.5 Å (center), and 7.5–15 Å (right) and correspond to regions identified in Figs. 3 and 5. Isosurfaces are at 4 (blue), 16 (yellow), and 64 times (orange) the bulk density. To see this figure in color, go online. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 3 Construction of 2D untwisted density distributions. (A and B) Helical disposition of DNA basepairs (A) leads to a convoluted map of Na+ ions (B). (C) Removing the helical twist angle Ω (i.e., untwisting) for each plane perpendicular to the main axis leads to a better resolved average distribution. Untwisting has a relatively minor effect on the relative distribution of atoms belonging to an average basepair, as shown by the dot clusters (red, oxygen; blue, nitrogen; gray, carbon; yellow, phosphorus). For example, although the C1′ atoms (green circles) are distributed nearly uniformly along a circle in the original mapping (B), untwisting leads to two localized positions (C). Numbered regions are discussed in text. (D) Orientation of typical basepairs. The ion densities shown here are derived from calculations using a bulk sodium chloride concentration of 0.17 M. The color scale for ion density can be found in Fig. 4. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 4 Untwisted ion and water normalized density distributions at 0.17 M NaCl. Results from MD with SPC/E (left), 3D-RISM-PSE-4 (middle), and NLPB (right) for sodium (upper row), chloride (middle row), and water oxygen (lower row). Due to the continuum treatment of the water dielectric effect, it is not possible to determine the distribution of water from NLPB theory in a straightforward manner. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 5 Na+ cylindrical RDFs obtained from explicit-solvent MD simulations (left), 3D-RISM (middle), and NLPB (right) at ∼0.2 M (upper) and ∼0.73 M (lower). A cylindrical subvolume (r=40Å and z=60Å) of the simulations was used to avoid end effects. Note that the normalization factor (salt bulk concentration) is slightly different (see Table S2) for each combination of water and ion models. To see this figure in color, go online. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions

Figure 6 Comparison between theoretical estimates of Na+ (left) and Cl− (right) PIPs and experimental results from Bai et al. (4). To see this figure in color, go online. Biophysical Journal 2014 106, 883-894DOI: (10.1016/j.bpj.2014.01.021) Copyright © 2014 Biophysical Society Terms and Conditions