Skip to main content
SpringerLink
Log in

Protein polarization effects in the thermodynamic computation of vibrational Stark shifts

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

Vibrational Stark effect (VSE) spectroscopy provides a direct measure of electrostatic fields within proteins. VSE also provides a unique way, still underutilized, to test the accuracy of electrostatic interactions in realistic finite-temperature simulations. Here, we quantify the electrostatic contributions of residues surrounding the catalytic reaction center in ketosteroid isomerase. Our goal is to understand how inter-residue charge transfer and local and non-local polarization affect the electric field at a molecular probe inside the protein. In particular, we show that polarization effects and charge transfer are essential to capture the correct thermodynamic structural average, which in turn affects the Stark shift.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Scheme 1
Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Benkovic SJ, Hammes-Schiffer S (2003) Science 301:1196–1202

    Article  CAS  Google Scholar 

  2. Hong H, Szabo G, Tamm LK (2006) Nat Chem Biol 2:627–635

    Article  CAS  Google Scholar 

  3. Shaik S, Ramanan R, Danovich D, Mandal D (2018) Chem Soc Rev 47:5125–5145

    Article  CAS  Google Scholar 

  4. Shaik S, Mandal D, Ramanan R (2016) Nat Chem 8:1091

    Article  CAS  Google Scholar 

  5. Lai W, Chen H, Cho K-B, Shaik S (2010) J Phys Chem Lett 1:2082–2087

    Article  CAS  Google Scholar 

  6. Shaik S, de Visser SP, Kumar D (2004) J Am Chem Soc 126:11746–11749

    Article  CAS  Google Scholar 

  7. Fried SD, Bagchi S, Boxer SG (2014) Science 346:1510–1514

    Article  CAS  Google Scholar 

  8. Park ES, Andrews SS, Hu RB, Boxer SG (1999) J Phys Chem B 103:9813–9817

    Article  CAS  Google Scholar 

  9. Plattner N, Meuwly M (2008) Biophys J 94:2505–2515

    Article  CAS  Google Scholar 

  10. Wang X, Zhang JZH, He X (2017) Chin J Chem Phys 30:705–716

    Article  Google Scholar 

  11. Wang X, He X, Zhang JZH (2013) J Phys Chem A 117:6015–6023

    Article  CAS  Google Scholar 

  12. Wang X, Zhang JZH, He X (2015) J Chem Phys 143:184111–184121

    Article  Google Scholar 

  13. Webb LJ, Boxer SG (2008) Biochemistry 47:1588–1598

    Article  CAS  Google Scholar 

  14. Xu L, Cohen AE, Boxer SG (2011) Biochemistry 50:8311–8322

    Article  CAS  Google Scholar 

  15. Sandberg DJ, Rudnitskaya AN, Gascón JA (2012) J Chem Theor Comput 8:2817–2823

    Article  CAS  Google Scholar 

  16. Muzet N, Guillot B, Jelsch C, Howard E, Lecomte C (2003) Proc Natl Acad Sci 100:8742

    Article  CAS  Google Scholar 

  17. Fournier B, Bendeif E-E, Guillot B, Podjarny A, Lecomte C, Jelsch C (2009) J Am Chem Soc 131:10929–10941

    Article  CAS  Google Scholar 

  18. Fried SD, Boxer SG (2015) Acc Chem Res 48:998–1006

    Article  CAS  Google Scholar 

  19. Wang X, He X (2018) Molecules 23:2410–2425

    Article  Google Scholar 

  20. Wu Y, Boxer SG (2016) J Am Chem Soc 138:11890–11895

    Article  CAS  Google Scholar 

  21. Matta CF (2014) J Comput Chem 35:1165–1198

    Article  CAS  Google Scholar 

  22. Fried SD, Bagchi S, Boxer SG (2013) J Am Chem Soc 135:11181–11192

    Article  CAS  Google Scholar 

  23. Saggu M, Levinson NM, Boxer SG (2011) J Am Chem Soc 133:17414–17419

    Article  CAS  Google Scholar 

  24. Suydam IT, Snow CD, Pande VS, Boxer SG (2006) Science 313:200–204

    Article  CAS  Google Scholar 

  25. Wang L, Fried SD, Boxer SG (2014) Proc Natl Acad Sci 111:18454–18459

    Article  CAS  Google Scholar 

  26. Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA (2018) Chem Rev 118:4071–4113

    Article  CAS  Google Scholar 

  27. Matta CF, Huang L, Massa L (2012) Future Med Chem 4:1873–1875

    Article  CAS  Google Scholar 

  28. Sowlati-Hashjin S, Matta CF (2014) J Chem Phys 141:039902

    Article  Google Scholar 

  29. Sowlati-Hashjin S, Matta CF (2013) J Chem Phys 139:144101

    Article  Google Scholar 

  30. Askerka M, Ho J, Batista ER, Gascón JA, Batista VS (2016) Methods Enzymol 577:443–481

    Article  CAS  Google Scholar 

  31. Gascón JA, Leung SSF, Batista ER, Batista VS (2006) J Chem Theor Comput 2:175–186

    Article  Google Scholar 

  32. Menikarachchi LC, Gascón JA (2008) J Mol Model 14:1–9

    Article  Google Scholar 

  33. Menikarachchi LC, Gascón JA (2011) J Mol Graph Model 30:38–45

    Article  CAS  Google Scholar 

  34. Wang X, Liu J, Zhang JZH, He X (2013) J Phys Chem A 117:7149–7161

    Article  CAS  Google Scholar 

  35. He X, Zhu T, Wang X, Liu J, Zhang JZH (2014) Acc Chem Res 47:2748–2757

    Article  CAS  Google Scholar 

  36. Schrodinger LLC (2016) Maestro 2016

  37. Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) J Chem Theor Comput 7:525–537

    Article  CAS  Google Scholar 

  38. Madhavi Sastry G, Adzhigirey M, Day T, Annabhimoju R, Sherman W (2013) J Comput Aid Mold Des 27:221–234

    Article  CAS  Google Scholar 

  39. Murphy RB, Philipp DM, Friesner RA (2000) J Comput Chem 21:1442–1457

    Article  CAS  Google Scholar 

  40. Schrodinger LLC (2016) Qsite 6.1

  41. Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA (2016) J Chem Theor Comput 12:281–296

    Article  CAS  Google Scholar 

  42. Bowers KJ, Chow DE, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE, Presented at the SC ‘06: proceedings of the 2006 ACM/IEEE conference on supercomputing, 2006 (unpublished)

  43. Grossfield A, Zuckerman DM (2009) Annu Rep Comput Chem 5:23–48

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was partially supported by a grant from the National Science Foundation (CHE-1404998).

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Connecticut, Storrs, CT, 06269, USA

    Alissa M. Richard & José A. Gascón

Authors
  1. Alissa M. Richard
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. José A. Gascón
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to José A. Gascón.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 194 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Richard, A.M., Gascón, J.A. Protein polarization effects in the thermodynamic computation of vibrational Stark shifts. Theor Chem Acc 139, 9 (2020). https://doi.org/10.1007/s00214-019-2522-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00214-019-2522-2

Keywords

Search

Navigation