HIT Web Server: A Hybrid Method to Improve Electrostatic Calculations for Biomolecules

Overview

Journal Comput Struct Biotechnol J

Specialty Biotechnology

Date 2022 Apr 15

PMID 35422969

Authors

Shengjie Sun

Juan A Lopez

Yixin Xie

Wenhan Guo

Dongfang Liu

Lin Li

Affiliations

Soon will be listed here.

Abstract

The electrostatic features of highly charged biomolecules are crucial and challenging tasks in computational biophysics. The electrostatic calculations by traditional implicit solvent methods are efficient but have difficulties on highly charged biomolecules. We have developed a Hybridizing Ion Treatment (HIT) tool, which successfully hybridizes the explicit ions and implicit solvation model to accurately calculate the electrostatic potential for highly charged biomolecules. Here we implemented the HIT tool into a web server. In this study, a training set was prepared to optimize the number of frames for the HIT web server. The results on tubulins, DNAs, and RNAs, reveal the mechanisms for the motor proteins, DNA of HIV, and tRNA. This HIT web server can be widely used to study highly charged biomolecules, including DNAs, RNAs, molecular motors, and other highly charged biomolecules.

Citing Articles

A Comparative Analysis of SARS-CoV-2 Variants of Concern (VOC) Spike Proteins Interacting with hACE2 Enzyme.

Chen J, Chen L, Quan H, Lee S, Khan K, Xie Y Int J Mol Sci. 2024; 25(15).

PMID: 39125601 PMC: 11311974. DOI: 10.3390/ijms25158032.

A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape.

Sun S, Rodriguez G, Zhao G, Sanchez J, Guo W, Du D Brief Bioinform. 2024; 25(2).

PMID: 38446738 PMC: 10939344. DOI: 10.1093/bib/bbae079.

Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.

Guo W, Du D, Zhang H, Sanchez J, Sun S, Xu W Biophys J. 2023; 123(17):2740-2748.

PMID: 38160255 PMC: 11393710. DOI: 10.1016/j.bpj.2023.12.024.

HIT-2: Implementing machine learning algorithms to treat bound ions in biomolecules.

Sun S, Xu H, Xie Y, Sanchez J, Guo W, Liu D Comput Struct Biotechnol J. 2023; 21:1383-1389.

PMID: 36817955 PMC: 9929202. DOI: 10.1016/j.csbj.2023.02.013.

Electrostatics in Computational Biophysics and Its Implications for Disease Effects.

Sun S, Poudel P, Alexov E, Li L Int J Mol Sci. 2022; 23(18).

PMID: 36142260 PMC: 9499338. DOI: 10.3390/ijms231810347.

References

van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark A, Berendsen H . GROMACS: fast, flexible, and free. J Comput Chem. 2005; 26(16):1701-18. DOI: 10.1002/jcc.20291. View

Sun S, Karki C, Gao B, Li L . Molecular mechanisms of cardiac actomyosin transforming from rigor state to post-rigor state. J Chem Phys. 2022; 156(3):035101. PMC: 9305598. DOI: 10.1063/5.0078166. View

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

Salie Z, Kirby K, Michailidis E, Marchand B, Singh K, Rohan L . Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA). Proc Natl Acad Sci U S A. 2016; 113(33):9274-9. PMC: 4995989. DOI: 10.1073/pnas.1605223113. View

Hingerty B, Brown R, Jack A . Further refinement of the structure of yeast tRNAPhe. J Mol Biol. 1978; 124(3):523-34. DOI: 10.1016/0022-2836(78)90185-7. View

Phillips J, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E . Scalable molecular dynamics with NAMD. J Comput Chem. 2005; 26(16):1781-802. PMC: 2486339. DOI: 10.1002/jcc.20289. View

Li L, Li C, Sarkar S, Zhang J, Witham S, Zhang Z . DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys. 2012; 5:9. PMC: 3463482. DOI: 10.1186/2046-1682-5-9. View

Xie Y, Karki C, Chen J, Liu D, Li L . Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA. Front Mol Biosci. 2021; 8:718587. PMC: 8377759. DOI: 10.3389/fmolb.2021.718587. View

Li L, Chakravorty A, Alexov E . DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding. J Comput Chem. 2017; 38(9):584-593. PMC: 5315605. DOI: 10.1002/jcc.24715. View

10.

Bertrand T, Kothe M, Liu J, Dupuy A, Rak A, Berne P . The crystal structures of TrkA and TrkB suggest key regions for achieving selective inhibition. J Mol Biol. 2012; 423(3):439-53. DOI: 10.1016/j.jmb.2012.08.002. View

11.

Li L, Jia Z, Peng Y, Godar S, Getov I, Teng S . Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations. Sci Rep. 2017; 7(1):8237. PMC: 5557957. DOI: 10.1038/s41598-017-08419-7. View

12.

Price D, Brooks 3rd C . A modified TIP3P water potential for simulation with Ewald summation. J Chem Phys. 2004; 121(20):10096-103. DOI: 10.1063/1.1808117. View

13.

Huang J, MacKerell Jr A . CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J Comput Chem. 2013; 34(25):2135-45. PMC: 3800559. DOI: 10.1002/jcc.23354. View

14.

Li L, Alper J, Alexov E . Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions. Sci Rep. 2016; 6:31523. PMC: 4987762. DOI: 10.1038/srep31523. View

15.

Sun S, Karki C, Xie Y, Xian Y, Guo W, Gao B . Hybrid method for representing ions in implicit solvation calculations. Comput Struct Biotechnol J. 2021; 19:801-811. PMC: 7847951. DOI: 10.1016/j.csbj.2021.01.020. View

16.

Schofield P, Zamecnik P . Cupric ion catalysis in hydrolysis of aminoacyl-tRNA. Biochim Biophys Acta. 1968; 155(2):410-6. DOI: 10.1016/0005-2787(68)90185-8. View

17.

Guo W, Xie Y, Lopez-Hernandez A, Sun S, Li L . Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2. Math Biosci Eng. 2021; 18(3):2372-2383. PMC: 8279046. DOI: 10.3934/mbe.2021120. View

18.

Dolinsky T, Nielsen J, McCammon J, Baker N . PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res. 2004; 32(Web Server issue):W665-7. PMC: 441519. DOI: 10.1093/nar/gkh381. View

19.

Shoichet B, Baase W, Kuroki R, Matthews B . A relationship between protein stability and protein function. Proc Natl Acad Sci U S A. 1995; 92(2):452-6. PMC: 42758. DOI: 10.1073/pnas.92.2.452. View

20.

Rao V, Srinivas K, Sujini G, Kumar G . Protein-protein interaction detection: methods and analysis. Int J Proteomics. 2014; 2014:147648. PMC: 3947875. DOI: 10.1155/2014/147648. View