Literature DB >> 23329894

Theory and Simulation of Multicomponent Osmotic Systems.

Sadish Karunaweera1, Moon Bae Gee, Samantha Weerasinghe, Paul E Smith.   

Abstract

Most cellular processes occur in systems containing a variety of components many of which are open to material exchange. However, computer simulations of biological systems are almost exclusively performed in systems closed to material exchange. In principle, the behavior of biomolecules in open and closed systems will be different. Here, we provide a rigorous framework for the analysis of experimental and simulation data concerning open and closed multicomponent systems using the Kirkwood-Buff (KB) theory of solutions. The results are illustrated using computer simulations for various concentrations of the solutes Gly, Gly(2) and Gly(3) in both open and closed systems, and in the absence or presence of NaCl as a cosolvent. In addition, KB theory is used to help rationalize the aggregation properties of the solutes. Here one observes that the picture of solute association described by the KB integrals, which are directly related to the solution thermodynamics, and that provided by more physical clustering approaches are different. It is argued that the combination of KB theory and simulation data provides a simple and powerful tool for the analysis of complex multicomponent open and closed systems.

Entities:  

Year:  2012        PMID: 23329894      PMCID: PMC3544414          DOI: 10.1021/ct300079v

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  18 in total

1.  Stabilization of proteins in confined spaces.

Authors:  H X Zhou; K A Dill
Journal:  Biochemistry       Date:  2001-09-25       Impact factor: 3.162

2.  Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components.

Authors:  Serge N Timasheff
Journal:  Proc Natl Acad Sci U S A       Date:  2002-07-03       Impact factor: 11.205

3.  Estimating hydration changes upon biomolecular reactions from osmotic stress, high pressure, and preferential hydration experiments.

Authors:  Seishi Shimizu
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-19       Impact factor: 11.205

4.  A contribution to the theory of preferential interaction coefficients.

Authors:  J Michael Schurr; David P Rangel; Sergio R Aragon
Journal:  Biophys J       Date:  2005-07-29       Impact factor: 4.033

Review 5.  Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences.

Authors:  Huan-Xiang Zhou; Germán Rivas; Allen P Minton
Journal:  Annu Rev Biophys       Date:  2008       Impact factor: 12.981

6.  Kirkwood-Buff theory of molecular and protein association, aggregation, and cellular crowding.

Authors:  Moon Bae Gee; Paul E Smith
Journal:  J Chem Phys       Date:  2009-10-28       Impact factor: 3.488

7.  Fluctuation theory of molecular association and conformational equilibria.

Authors:  Yuanfang Jiao; Paul E Smith
Journal:  J Chem Phys       Date:  2011-07-07       Impact factor: 3.488

8.  A Pairwise Preferential Interaction Model for Understanding Peptide Aggregation.

Authors:  Myungshim Kang; Paul Edward Smith
Journal:  Int J Thermophys       Date:  2010-05-01       Impact factor: 1.608

9.  Developing Force Fields from the Microscopic Structure of Solutions.

Authors:  Elizabeth A Ploetz; Nikolaos Bentenitis; Paul E Smith
Journal:  Fluid Phase Equilib       Date:  2010-03-25       Impact factor: 2.775

10.  Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas.

Authors:  Jonathan G Cannon; Charles F Anderson; M Thomas Record
Journal:  J Phys Chem B       Date:  2007-07-21       Impact factor: 2.991

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  8 in total

1.  Local Fluctuations in Solution: Theory and Applications.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  Adv Chem Phys       Date:  2013       Impact factor: 1.000

2.  Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization.

Authors:  Mark S Miller; Wesley K Lay; Adrian H Elcock
Journal:  J Phys Chem B       Date:  2016-04-21       Impact factor: 2.991

3.  Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other.

Authors:  Casey T Andrews; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2013-10-08       Impact factor: 6.006

4.  Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  J Chem Phys       Date:  2015-03-07       Impact factor: 3.488

5.  Reparametrization of Protein Force Field Nonbonded Interactions Guided by Osmotic Coefficient Measurements from Molecular Dynamics Simulations.

Authors:  Mark S Miller; Wesley K Lay; Shuxiang Li; William C Hacker; Jiadi An; Jianlan Ren; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2017-03-27       Impact factor: 6.006

6.  Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements.

Authors:  Wesley K Lay; Mark S Miller; Adrian H Elcock
Journal:  J Chem Theory Comput       Date:  2016-03-22       Impact factor: 6.006

7.  Synergy in protein-osmolyte mixtures.

Authors:  Jörg Rösgen
Journal:  J Phys Chem B       Date:  2014-12-17       Impact factor: 2.991

8.  Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein.

Authors:  Pallavi Banerjee; Reinhard Lipowsky; Mark Santer
Journal:  J Chem Theory Comput       Date:  2020-05-26       Impact factor: 6.006

  8 in total

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