Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

Journal of the American Chemical Society
Jianhan ChenCharles L Brooks

Abstract

The efficient and accurate characterization of solvent effects is a key element in the theoretical and computational study of biological problems. Implicit solvent models, particularly generalized Born (GB) continuum electrostatics, have emerged as an attractive tool to study the structure and dynamics of biomolecules in various environments. Despite recent advances in this methodology, there remain limitations in the parametrization of many of these models. In the present work, we demonstrate that it is possible to achieve a balanced implicit solvent force field by further optimizing the input atomic radii in combination with adjusting the protein backbone torsional energetics. This parameter optimization is guided by the potentials of mean force (PMFs) between amino acid polar groups, calculated from explicit solvent free energy simulations, and by conformational equilibria of short peptides, obtained from extensive folding and unfolding replica exchange molecular dynamics (REX-MD) simulations. Through the application of this protocol, the delicate balance between the competing solvation forces and intramolecular forces appears to be better captured, and correct conformational equilibria for a range of both helical and beta-h...Continue Reading

References

Oct 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·R A GoldsteinP G Wolynes
Jun 5, 1982·Journal of Molecular Biology·J Warwicker, H C Watson
Sep 1, 1994·Nature Structural Biology·F J BlancoL Serrano
May 26, 1995·Science·B Honig, A Nicholls
Oct 6, 1997·Science·B I Dahiyat, S L Mayo
Nov 21, 1997·Nature·V MuñozW A Eaton
May 14, 1999·Current Opinion in Structural Biology·U H Hansmann, Y Okamoto
Apr 8, 2000·Current Opinion in Structural Biology·T Lazaridis, M Karplus
Oct 14, 2000·Annual Review of Physical Chemistry·D Bashford, D A Case
Apr 12, 2001·Current Opinion in Structural Biology·T Simonson
May 2, 2001·Proceedings of the National Academy of Sciences of the United States of America·A G CochranM A Starovasnik
Sep 8, 2001·Journal of Molecular Biology·M López de la PazL Serrano
Oct 17, 2001·Journal of Molecular Biology·B ZagrovicV Pande
Feb 19, 2002·Chemical Reviews·Christopher J. Cramer, Donald G. Truhlar
Apr 30, 2002·Nature Structural Biology·Jonathan W NeidighNiels H Andersen
Sep 5, 2002·Journal of Computational Chemistry·Ray LuoMichael K Gilson
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
Feb 13, 2003·Journal of the American Chemical Society·Artëm Masunov, Themis Lazaridis
Mar 14, 2003·Journal of Molecular Biology·Shibasish ChowdhuryYong Duan
Jun 17, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jed W Pitera, William Swope
Sep 10, 2003·Journal of Computational Chemistry·Wonpil ImCharles L Brooks
Nov 13, 2003·Physical Review Letters·A SchugW Wenzel
Nov 18, 2003·Proceedings of the National Academy of Sciences of the United States of America·Hugh Nymeyer, Angel E García
Nov 20, 2003·Journal of the American Chemical Society·Paolo CarnevaliSiavash N Meshkat
Jan 22, 2004·Journal of the American Chemical Society·Alexander D MacKerellCharles L Brooks
Jan 22, 2004·Journal of Computational Chemistry·Emilio Gallicchio, Ronald M Levy
Jan 27, 2004·Journal of Molecular Biology·Wei Yuan YangMartin Gruebele
Feb 12, 2004·Journal of the American Chemical Society·Jakob P Ulmschneider, William L Jorgensen
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
Jul 21, 2004·Journal of Computational Chemistry·Alexander D Mackerell
Jul 23, 2004·The Journal of Chemical Physics·Michael FeigCharles L Brooks
Sep 21, 2004·Biophysical Journal·Alfonso Jaramillo, Shoshana J Wodak

❮ Previous
Next ❯

Citations

Dec 4, 2010·Journal of Molecular Modeling·Meng-Juei Hsieh, Ray Luo
Oct 12, 2012·Journal of Molecular Modeling·Gaurav BhattiYeshitila Gebremichael
Nov 2, 2011·Journal of Computer-aided Molecular Design·Despina LaimouTheodore V Tselios
Sep 17, 2013·Journal of Molecular Graphics & Modelling·Michael Feig, Yuji Sugita
Dec 12, 2012·Quarterly Reviews of Biophysics·Pengyu RenNathan A Baker
Jan 13, 2011·Biochemistry·D Victoria WilliamsNiels H Andersen
Jul 17, 2012·Journal of Chemical Information and Modeling·Laura Delgado-SolerJaime Rubio-Martinez
Nov 17, 2011·Journal of the American Chemical Society·Garrett B GohCharles L Brooks
Dec 1, 2011·The Journal of Physical Chemistry. B·Hanzhong Liu, Shuanghong Huo
Sep 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Xiang GaoYu-Zhong Zhang
Sep 22, 2012·The Journal of Biological Chemistry·Joong-Youn ShimDebra A Kendall
Jan 22, 2008·Protein Engineering, Design & Selection : PEDS·Bipasha BaruaNiels H Andersen
Jul 10, 2008·Journal of the Royal Society, Interface·Marc W van der KampAdrian J Mulholland
Mar 21, 2007·BMC Structural Biology·Abhinav Verma, Wolfgang Wenzel
May 24, 2014·PLoS Computational Biology·Drazen Petrov, Bojan Zagrovic
May 17, 2007·PloS One·Alex KentsisRoman Osman
Oct 12, 2013·PloS One·Atanu MaityShubhra Ghosh Dastidar
Jul 8, 2009·International Journal of Molecular Sciences·Yi XiaoYi He
Jan 1, 2010·International Journal of Molecular Sciences·Timothy H ClickJianhan Chen
Mar 24, 2011·Future Medicinal Chemistry·Predrag Kukić, Jens Erik Nielsen
May 3, 2011·The Journal of Chemical Physics·Alexey V Onufriev, Grigori Sigalov
Apr 17, 2009·The Journal of Chemical Physics·Qin CaiRay Luo
Mar 19, 2008·The Journal of Chemical Physics·Soonmin JangYoungshang Pak
Mar 19, 2008·The Journal of Chemical Physics·Abhinav Verma, Wolfgang Wenzel
May 12, 2009·The Journal of Chemical Physics·Xianfeng LiSteven J Stuart
Nov 10, 2009·The Journal of Chemical Physics·Hongxing LeiYong Duan
Sep 14, 2013·The Journal of Chemical Physics·Li XiaoRay Luo
May 2, 2009·The Journal of Chemical Physics·Yuguang Mu
Jul 19, 2013·The Journal of Chemical Physics·Yanxiang ZhaoJ Andrew McCammon
Oct 19, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jana Khandogin, Charles L Brooks
Nov 23, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jana KhandoginCharles L Brooks
Feb 10, 2007·Journal of the American Chemical Society·Jianhan Chen, Charles L Brooks
Dec 15, 2010·Proceedings of the National Academy of Sciences of the United States of America·Mark M ChenBarbara Imperiali
Jul 21, 2015·Protein Science : a Publication of the Protein Society·Fumitaka KamoNobuyuki Matubayasi
Dec 21, 2010·Journal of Molecular Graphics & Modelling·Yi ShangCarlos Simmerling
Jul 16, 2008·Journal of Molecular Graphics & Modelling·Won-Joon SonSeokmin Shin

❮ 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.

Related Papers

Journal of Computational Chemistry
Wonpil ImCharles L Brooks
Proceedings of the National Academy of Sciences of the United States of America
Jana KhandoginCharles L Brooks
Journal of the American Chemical Society
Carlos SimmerlingAdrian Roitberg
© 2021 Meta ULC. All rights reserved