Improved Generalized Born Solvent Model Parameters for Protein Simulations

Journal of Chemical Theory and Computation
Hai NguyenCarlos Simmerling

Abstract

The generalized Born (GB) model is one of the fastest implicit solvent models and it has become widely adopted for Molecular Dynamics (MD) simulations. This speed comes with tradeoffs, and many reports in the literature have pointed out weaknesses with GB models. Because the quality of a GB model is heavily affected by empirical parameters used in calculating solvation energy, in this work we have refit these parameters for GB-Neck, a recently developed GB model, in order to improve the accuracy of both the solvation energy and effective radii calculations. The data sets used for fitting are significantly larger than those used in the past. Comparing to other pairwise GB models like GB-OBC and the original GB-Neck, the new GB model (GB-Neck2) has better agreement to Poisson-Boltzmann (PB) in terms of reproducing solvation energies for a variety of systems ranging from peptides to proteins. Secondary structure preferences are also in much better agreement with those obtained from explicit solvent MD simulations. We also obtain near-quantitative reproduction of experimental structure and thermal stability profiles for several model peptides with varying secondary structure motifs. Extension to non-protein systems will be explored...Continue Reading

References

Apr 5, 1987·Journal of Molecular Biology·S Vijay-KumarW J Cook
Sep 1, 1994·Nature Structural Biology·F J BlancoL Serrano
Mar 1, 1997·Nature Structural Biology·C J McKnightP S Kim
May 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·A G CochranM A Starovasnik
Jul 27, 2001·Acta Crystallographica. Section D, Biological Crystallography·C SauterJ M García-Ruiz
Apr 30, 2002·Nature Structural Biology·Jonathan W NeidighNiels H Andersen
Sep 6, 2002·Journal of Computational Chemistry·Alexey OnufrievDonald Bashford
Sep 19, 2002·Journal of the American Chemical Society·Carlos SimmerlingAdrian E Roitberg
Sep 21, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ruhong Zhou, Bruce J Berne
Dec 17, 2002·Journal of Computational Chemistry·Asim OkurCarlos Simmerling
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jed W Pitera, William Swope
Jul 18, 2003·Journal of Computational Chemistry·Bojan Zagrovic, Vijay Pande
Oct 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·Ruhong Zhou
Nov 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Hugh Nymeyer, Angel E García
Apr 20, 2004·Current Opinion in Structural Biology·Michael Feig, Charles L Brooks
Jun 10, 2004·Journal of the American Chemical Society·R Matthew FesinmeyerNiels H Andersen
Apr 20, 2005·The Journal of Chemical Physics·Grigori SigalovAlexey Onufriev
May 17, 2005·Proceedings of the National Academy of Sciences of the United States of America·Thang K ChiuDavid R Davies
Aug 13, 2005·Journal of Molecular Biology·Daniel R RoeCarlos Simmerling
Jan 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Viktor HornakCarlos Simmerling
May 20, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jason A Wagoner, Nathan A Baker
Jul 21, 2006·The Journal of Physical Chemistry. B·Jiang ZhuBarry Honig
Feb 10, 2007·Journal of the American Chemical Society·Jianhan Chen, Charles L Brooks
Mar 21, 2007·Journal of the American Chemical Society·Scott A Showalter, Rafael Brüschweiler
Nov 21, 2007·The Journal of Chemical Physics·John MonganAlexey Onufriev
Jan 10, 2008·Physical Chemistry Chemical Physics : PCCP·Jianhan Chen, Charles L Brooks
May 13, 2008·The Journal of Physical Chemistry. B·M Scott ShellKen A Dill
Nov 14, 2008·Proceedings of the National Academy of Sciences of the United States of America·Dietmar PaschekAngel E García
Feb 5, 2009·Journal of Computational Chemistry·Mark S FriedrichsVijay S Pande
Aug 5, 2009·Biophysical Journal·Lauren WickstromCarlos Simmerling
Feb 6, 2010·The Journal of Physical Chemistry. B·Meng-Juei Hsieh, Ray Luo
Apr 27, 2010·Journal of Chemical Theory and Computation·Emilio GallicchioRonald M Levy
Jul 21, 2010·Biophysical Journal·Oliver F LangeBert L de Groot
Jan 1, 2007·Journal of Chemical Theory and Computation·John MonganAlexey Onufriev

❮ Previous
Next ❯

Citations

Jan 21, 2016·Biochemistry·Kelly E Du PontChristopher E Berndsen
Jan 17, 2016·Current Opinion in Structural Biology·Alberto PerezKen A Dill
May 24, 2015·FEBS Letters·Tracy A CaldwellNathan T Wright
Dec 23, 2015·Journal of Chemical Theory and Computation·Jakub Kaminsky, Frank Jensen
Oct 28, 2015·Protein Science : a Publication of the Protein Society·Grace H PhamEric R Strieter
Sep 10, 2015·Proceedings of the National Academy of Sciences of the United States of America·Alberto PerezKen A Dill
Aug 11, 2015·Journal of Molecular Recognition : JMR·Lauren WickstromRonald M Levy
Jul 21, 2015·Protein Science : a Publication of the Protein Society·Duy P HuaCarol Beth Post
Nov 8, 2014·Chemical Biology & Drug Design·Cassandra D M ChurchillJack A Tuszynski
Nov 18, 2015·Journal of Chemical Theory and Computation·Haiyang ZhangDavid van der Spoel
Nov 18, 2015·Journal of Chemical Theory and Computation·Alberto PerezKen A Dill
Sep 4, 2015·Biophysical Journal·Jameson R BotheJohn L Markley
Nov 18, 2015·Journal of Chemical Theory and Computation·Hai NguyenCarlos Simmerling
Jul 3, 2015·The Journal of Physical Chemistry. B·Elif Nihal KorkmazQiang Cui
Mar 22, 2015·Origins of Life and Evolution of the Biosphere : the Journal of the International Society for the Study of the Origin of Life·Akifumi Oda, Shuichi Fukuyoshi
Aug 1, 2015·Journal of Biomolecular Structure & Dynamics·Cassandra D M ChurchillJack A Tuszynski
May 18, 2016·Analytical Chemistry·Edward J BasomMegan C Thielges
May 4, 2016·The Journal of Physical Chemistry. B·Wenhui XiUlrich H E Hansmann
Aug 9, 2016·Journal of Chemical Information and Modeling·Irene Maffucci, Alessandro Contini
Oct 17, 2015·Proteins·InSuk JoungJooyoung Lee
Sep 15, 2016·Journal of Chemical Information and Modeling·Haiyang ZhangDavid van der Spoel
Oct 13, 2016·Journal of Chemical Theory and Computation·Melina K RobinsonM Scott Shell
Dec 6, 2016·International Journal of Molecular Sciences·Geoffrey M GrayGregory P Holland
Jan 3, 2016·The Journal of Chemical Physics·N Ceres, R Lavery
Jan 4, 2017·Journal of Chemical Theory and Computation·Joseph A MorroneKen A Dill
Jan 4, 2017·Journal of Chemical Theory and Computation·Joseph A MorroneKen A Dill
Feb 24, 2017·PLoS Computational Biology·Alice R WalkerGerardo Andrés Cisneros
Dec 22, 2016·Protein Science : a Publication of the Protein Society·Haydeé Mesa-GallosoPedro A Valiente
Mar 16, 2017·Journal of Chemical Theory and Computation·Hui LiuTingjun Hou
Apr 21, 2017·The Journal of Physical Chemistry. B·Yukinobu MizuharaMitsunori Takano
May 13, 2017·Journal of Chemical Theory and Computation·Piotr Setny, Anita Dudek
Apr 24, 2015·Physical Chemistry Chemical Physics : PCCP·A Kyrychenko
Nov 8, 2017·International Journal of Molecular Sciences·Katarzyna RetzerChristian Luschnig
Oct 13, 2017·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Koichi KatoAkifumi Oda
Nov 8, 2017·Nature Communications·Nicholas P ReynoldsRaffaele Mezzenga
Jun 28, 2018·Physical Chemistry Chemical Physics : PCCP·Qiang Shao, Weiliang Zhu
Oct 1, 2014·Journal of Computational Chemistry·Fabian Zeller, Martin Zacharias

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.