1932

Abstract

Electrostatics play an important role in many aspects of protein chemistry. However, the accurate determination of side chain proton affinity in proteins by experiment and theory remains challenging. In recent years the field of nuclear magnetic resonance spectroscopy has advanced the way that protonation states are measured, allowing researchers to examine electrostatic interactions at an unprecedented level of detail and accuracy. Experiments are now in place that follow pH-dependent 13C and 15N chemical shifts as spatially close as possible to the sites of protonation, allowing all titratable amino acid side chains to be probed sequence specifically. The strong and telling response of carefully selected reporter nuclei allows individual titration events to be monitored. At the same time, improved frameworks allow researchers to model multiple coupled protonation equilibria and to identify the underlying pH-dependent contributions to the chemical shifts.

Loading

Article metrics loading...

/content/journals/10.1146/annurev-biophys-083012-130351
2015-06-22
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/biophys/44/1/annurev-biophys-083012-130351.html?itemId=/content/journals/10.1146/annurev-biophys-083012-130351&mimeType=html&fmt=ahah

Literature Cited

  1. Alberty RA. 1.  2000. Effect of pH on protein–ligand equilibria. J. Phys. Chem. B 104:9929–34 [Google Scholar]
  2. Alexov E, Mehler EL, Baker N, Baptista AM, Huang Y. 2.  et al. 2011. Progress in the prediction of pKa values in proteins. Proteins 79:3260–75 [Google Scholar]
  3. Anandakrishnan R, Aguilar B, Onufriev AV. 3.  2012. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res. 40:W537–41 [Google Scholar]
  4. André I, Linse S, Mulder FAA. 4.  2007. Residue-specific pKa determination of lysine and arginine side chains by indirect 15N and 13C spectroscopy: application to apo calmodulin. J. Am. Chem. Soc. 129:15805–13Performs an H2(C)N experiment to study lysine, arginine, and N terminus pKa constants. [Google Scholar]
  5. Antosiewicz J, McCammon JW, Gilson MK. 5.  1994. Prediction of pH-dependent properties of proteins. J. Mol. Biol. 238:415–36 [Google Scholar]
  6. Baturin SJ, Okon M, McIntosch LP. 6.  2011. Structure, dynamics, and ionization equilibria of the tyrosine residues in Bacillus circulans xylanase. J. Biomol. NMR 51:379–94 [Google Scholar]
  7. Bombarda E, Ullmann GM. 7.  2010. pH-dependent pKa values in proteins—a theoretical analysis of protonation energies with practical consequences for enzymatic reactions. J. Phys. Chem. B 114:1994–2003 [Google Scholar]
  8. Boyd J, Domene C, Redfield C, Ferraro MB, Lazzeretti P. 8.  2003. Calculation of dipole-shielding polarizability (σIαβγ): the influence of uniform electric field effects on the shielding of backbone nuclei in proteins. J. Am. Chem. Soc. 125:9556–57Makes quantum mechanical calculations of the polarizability due to nuclear shielding. [Google Scholar]
  9. Buckingham AD. 9.  1960. Chemical shifts in the nuclear magnetic resonance spectra of molecules containing polar groups. Can. J. Chem. 38:300–7 [Google Scholar]
  10. Castaneda CA, Fitch CA, Majumdar A, Khangulov V, Schlessman JL. 10.  et al. 2009. Molecular determinants of the pKa values of Asp and Glu residues in staphylococcal nuclease. Proteins 77:570–88 [Google Scholar]
  11. Chivers PT, Prehoda KE, Volkman BF, Kim BM, Markley JL, Raines RT. 11.  1997. Microscopic pKa values of Escherichia coli thioredoxin. Biochemistry 36:14985–91 [Google Scholar]
  12. Croke RL, Patil SM, Quevreaux J, Kendall DA, Alexandrescu AT. 12.  2011. NMR determination of pKa values in α-synuclein. Protein Sci. 20:256–69 [Google Scholar]
  13. Di Cera E. 13.  1998. Site-specific thermodynamics: understanding cooperativity in molecular recognition. Chem. Rev. 98:1563–91 [Google Scholar]
  14. Edsall JT, Martin RB, Hollingworth BR. 14.  1958. Ionization of individual groups in dibasic acids, with application to the amino and hydroxyl groups of tyrosine. PNAS 44:505–18 [Google Scholar]
  15. Farrell D, Miranda ES, Webb H, Georgi N, Crowley PB. 15.  et al. 2010. TitrationDB: storage and analysis of NMR-monitored protein pH titration curves. Proteins 78:843–57 [Google Scholar]
  16. Forman-Kay JD, Clore GM, Gronenborn AM. 16.  1992. Relationship between electrostatics and redox function in human thioredoxin: characterization of pH titration shifts using two-dimensional homo- and heteronuclear NMR. Biochemistry 31:3442–52 [Google Scholar]
  17. Gao G, Prasad R, Lodwig SN, Unkefer CJ, Beard WA. 17.  et al. 2006. Determination of lysine pK values using [5-13C]lysine: application to the lyase domain of DNA Pol β. J. Am. Chem. Soc. 128:8104–5 [Google Scholar]
  18. Harris TK, Turner GJ. 18.  2002. Structural basis of perturbed pKa values of catalytic groups in enzyme active sites. IUBMB Life 53:85–98 [Google Scholar]
  19. Hass MAS. 19.  2007. Motions in proteins on the microsecond time-scale characterized by NMR: applications to histidine dynamics in blue copper proteins PhD Thesis, Univ. Copenhagen
  20. Hass MAS, Christensen HEM, Zhang JD, Led JJ. 20.  2007. Kinetics and mechanism of the acid transition of the active site in plastocyanin. Biochemistry 46:14619–28 [Google Scholar]
  21. Hass MAS, Hansen DF, Christensen HEM, Led JJ, Kay LE. 21.  2008. Characterization of conformational exchange of a histidine side chain: protonation, rotamerization, and tautomerization of His61 in plastocyanin from Anabaena variabilis. J. Am. Chem. Soc. 130:8460–70Examines tautomers, rotamers, charge states, and proton exchange of histidine. [Google Scholar]
  22. Hass MAS, Jensen MR, Led JJ. 22.  2008. Probing electric fields in proteins in solution by NMR spectroscopy. Proteins 72:333–43Identifies electric field effects on chemical shifts. [Google Scholar]
  23. Hass MAS, Vlasie M, Ubbink M, Led JJ. 23.  2009. Conformational exchange in pseudoazurin: different kinds of microsecond to millisecond dynamics characterized by their pH and buffer dependence using 15N NMR relaxation. Biochemistry 48:50–58 [Google Scholar]
  24. Hass MAS, Yilmaz A, Christensen HEM, Led JJ. 24.  2009. Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion. J. Biomol. NMR 44:225–33 [Google Scholar]
  25. Henry GD, Sykes BD. 25.  1995. Determination of the rotational dynamics and pH dependence of the hydrogen exchange rates of the arginine guanidino group using NMR spectroscopy. J. Biomol. NMR 6:59–66 [Google Scholar]
  26. Honig B, Nicholls A. 26.  1995. Classical electrostatics in biology and chemistry. Science 268:1144–49 [Google Scholar]
  27. Hunter CA, Packer MJ, Zonta C. 27.  2005. From structure to chemical shift and vice-versa. Prog. Nucl. Magn. Reson. Spectrosc. 47:27–39 [Google Scholar]
  28. Huque ME, Vogel HJ. 28.  1993. Carbon-13 NMR studies of the lysine side chains of calmodulin and its proteolytic fragments. J. Protein Chem. 12:695–707 [Google Scholar]
  29. Jensen KS, Pedersen JT, Winther JR, Teilum K. 29.  2014. The pKa value and accessibility of cysteine residues are key determinants for protein substrate discrimination by glutaredoxin. Biochemistry 53:2533–40 [Google Scholar]
  30. Kato-Toma Y, Iwashita T, Masuda K, Oyama Y, Ishiguro M. 30.  2003. pKa measurements from nuclear magnetic resonance of tyrosine-150 in class C beta-lactamase. Biochem. J. 371:175–81 [Google Scholar]
  31. Klingen AR, Bombarda E, Ullmann GM. 31.  2006. Theoretical investigation of the behavior of titratable groups in proteins. Photochem. Photobiol. Sci. 5:588–96 [Google Scholar]
  32. Kukić P, Farrell D, Søndergaard CR, Bjarnadottir U, Bradley J. 32.  et al. 2009. Improving the analysis of NMR spectra tracking pH-induced conformational changes: removing artifacts of the electric field on the NMR chemical shift. Proteins 78:971–84Combines electrostatic models and chemical shift prediction to identify structural changes. [Google Scholar]
  33. Li SH, Hong M. 33.  2011. Protonation, tautomerization, and rotameric structure of histidine: a comprehensive study by magic-angle-spinning solid-state NMR. J. Am. Chem. Soc. 133:1534–44 [Google Scholar]
  34. Lindman S, Linse S, Mulder FAA, André I. 34.  2006. Electrostatic contributions to residue-specific protonation equilibria and proton binding capacitance for a small protein. Biochemistry 45:13993–4002Discusses proton binding capacitance and provides an explanation for the Hill parameter in pH titrations. [Google Scholar]
  35. Lindman S, Linse S, Mulder FAA, André I. 35.  2007. pKa values for side-chain carboxyl groups of a PGB1 variant explain salt and pH-dependent stability. Biophys. J. 92:257–66 [Google Scholar]
  36. Markley JL. 36.  1975. Observation of histidine residues in proteins by means of nuclear magnetic resonance spectroscopy. Acc. Chem. Res. 8:70–80 [Google Scholar]
  37. Martini JWR, Ullmann GM. 37.  2013. A mathematical view on the decoupled sites representation. J. Math. Biol. 66:477–503 [Google Scholar]
  38. McIntosh LP, Naito D, Baturin SJ, Okon M, Joshi MD, Nielsen JE. 38.  2011. Dissecting electrostatic interpretations in Bacillus circulans xylanase through NMR-monitored pH titrations. J. Biomol. NMR 51:5–19Investigates in great detail the electrostatic interaction between two active site residues. [Google Scholar]
  39. Mulder FA, Spronk CA, Slijper M, Kaptein R, Boelens R. 39.  1996. Improved HSQC experiments for the observation of exchange broadened signals. J. Biomol. NMR 8:223–28 [Google Scholar]
  40. Nielsen JE. 40.  2007. Analysing the pH-dependent properties of proteins using pKa calculations. J. Mol. Graph. Model. 25:691–99 [Google Scholar]
  41. Nielsen JE, Gunner MR, García-Moreno B. 41.  2011. The pKa Cooperative: a collaborative effort to advance structure-based calculations of pKa values and electrostatic effects in proteins. Proteins 79:3249–59Forms the pKa cooperative, a forum on protein electrostatics for experimentalists and theoreticians. [Google Scholar]
  42. Norton RS, Bradbury JH. 42.  1974. Carbon-13 nuclear magnetic resonance study of tyrosine titrations. J. Chem. Soc. Chem. Comm. 919:870–71 [Google Scholar]
  43. Oda Y, Yamazaki T, Nagayama K, Kanaya S, Kuroda Y, Nakamura H. 43.  1994. Individual ionization constants of all the carboxyl groups in ribonuclease HI from Escherichia coli determined by NMR. Biochemistry 33:5275–84Applies the H2(C)CO experiment to study carboxylate pKa constants. [Google Scholar]
  44. Oktaviani NA, Pool TJ, Kamikubo H, Slager J, Scheek RM. 44.  et al. 2012. Comprehensive determination of protein tyrosine pKa values for photoactive yellow protein using indirect 13C NMR spectroscopy. Biophys. J. 102:579–86 [Google Scholar]
  45. Onufriev A, Case DA, Ullmann GM. 45.  2001. A novel view of pH titration in biomolecules. Biochemistry 40:3413–19 [Google Scholar]
  46. Onufriev A, Ullmann GM. 46.  2004. Decomposing complex cooperative ligand binding into simple components: connections between microscopic and macroscopic models. J. Phys. Chem. 108:11157–69Describes the decoupled site representation. [Google Scholar]
  47. Pace CN, Grimsley GR, Scholtz JM. 47.  2009. Protein ionizable groups: pK values and their contribution to protein stability and solubility. J. Biol. Chem. 284:13285–89 [Google Scholar]
  48. Palmer AG 3rd, Kroenke CD, Loria JP. 48.  2001. Nuclear magnetic resonance methods for quantifying microsecond-to-millisecond motions in biological macromolecules. Methods Enzymol. 339:204–38 [Google Scholar]
  49. Paquin R, Ferrage F, Mulder FAA, Akke M, Bodenhausen G. 49.  2008. Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by 13C nuclear spin relaxation. J. Am. Chem. Soc. 130:15805–7 [Google Scholar]
  50. Pelton JG, Torchia DA, Meadow ND, Roseman S. 50.  1993. Tautomeric states of the active-site histidines of phosphorylated and unphosphorylated IIIGlc, a signal-transducing protein from Escherichia coli, using two-dimensional heteronuclear NMR techniques. Protein Sci. 2:543–58 [Google Scholar]
  51. Pérez-Cañadillas JM, Campos-Olivas R, Lacadcena J, Martínez del Pozo A, Gavilanes JG. 51.  et al. 1998. Characterization of pKa values and titration shifts in the cytotoxic ribonuclease α-sarcin by NMR. Relationship between electrostatic interactions, structure, and catalytic function. Biochemistry 37:15865–76 [Google Scholar]
  52. Perutz MF. 52.  1978. Electrostatic effects in proteins. Science 201:43621187–91 [Google Scholar]
  53. Platzer G, Okon M, McIntosh LP. 53.  2014. pH-dependent random coil 1H, 13C, and 15N chemical shifts of the ionizable amino acids: a guide for protein pKa measurements. J. Biomol. NMR 60:109–29 [Google Scholar]
  54. Pujato M, Navarro A, Versace R, Mancusso R, Ghose R, Tasayco ML. 54.  2006. The pH-dependence of amide chemical shift of Asp/Glu reflects its pKa in intrinsically disordered proteins with only local interactions. Biochim. Biophys. Acta 1764:1227–33 [Google Scholar]
  55. Richarz R, Wüthrich K. 55.  1978. Carbon-13 NMR chemical-shifts of common amino-acid residues measured in aqueous-solutions of linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers 17:2133–41 [Google Scholar]
  56. Rocchia W, Alexov E, Honig B. 56.  2001. Extending the applicability of the nonlinear Poisson-Boltzmann equation: multiple dielectric constants and multivalent ions. J. Phys. Chem. B 105:6507–14 [Google Scholar]
  57. Rocchia W, Sridharan S, Nicholls A, Alexov E, Chiabrera A, Honig B. 57.  2002. Rapid grid-based construction of the molecular surface for both molecules and geometric objects: applications to the finite difference Poisson-Boltzmann method. J. Comp. Chem. 23:128–37 [Google Scholar]
  58. Rostovtseva TK, Liu T, Colombini M, Parsegian VA, Bezrukov SM. 58.  2000. Positive cooperativity without domains or subunits in a monomeric membrane channel. PNAS 97:7819–22 [Google Scholar]
  59. Shrager RI, Cohen JS, Heller SR, Sachs DH, Schechter AN. 59.  1972. Mathematical models for interacting groups in nuclear magnetic resonance titration curves. Biochemistry 11:541–47 [Google Scholar]
  60. Søndergaard CR, McIntosh LP, Pollastri G, Nielsen JE. 60.  2008. Determination of electrostatic interaction energies and protonation state populations in enzyme active sites. J. Mol. Biol. 376:269–87 [Google Scholar]
  61. Spitzner N, Löhr F, Pfeiffer S, Koumanov A, Karshikoff A, Rüterjans H. 61.  2001. Ionization properties of titratable groups in ribonuclease T1. Eur. Biophys. J. 30:186–97 [Google Scholar]
  62. Sudmeier JL, Bradshaw EM, Haddad KE, Day RM, Thalhauser CJ. 62.  et al. 2003. Identification of histidine tautomers in proteins by 2D 1H/13Cδ2 one-bond correlated NMR. J. Am. Chem. Soc. 125:8430–31 [Google Scholar]
  63. Sudmeier JL, Evelhoch JL, Jonsson NB-H. 63.  1980. Dependence of NMR lineshape analysis upon chemical rates and mechanisms: implications for enzyme histidine titrations. J. Mag. Reson. 40:377–90 [Google Scholar]
  64. Sudmeier JL, Reilley CN. 64.  1964. Nuclear magnetic resonance studies of protonation of polyamine and aminocarboxylate compounds in aqueous solution. Anal. Chem. 36:1698–706 [Google Scholar]
  65. Szakács Z, Kraszni M, Noszál B. 65.  2004. Determination of microscopic acid-base parameters from NMR-pH titrations. Anal. Bioanal. Chem. 378:1428–48 [Google Scholar]
  66. Takeda M, Jee J, Ono AM, Terauchi T, Kainosho M. 66.  2009. Hydrogen exchange rate of tyrosine hydroxyl groups in proteins as studied by the deuterium isotope effect on Cζ chemical shifts. J. Am. Chem. Soc. 131:18556–62 [Google Scholar]
  67. Tollinger M, Crowhurst KA, Kay LE, Forman-Kay JD. 67.  2003. Site-specific contributions to the pH dependence of protein stability. PNAS 100:4545–50 [Google Scholar]
  68. Tomlinson JH, Green VL, Baker PJ, Williamson MP. 68.  2010. Structural origins of pH-dependent chemical shifts in the B1 domain of protein G. Proteins 14:3000–16 [Google Scholar]
  69. Ullmann GM. 69.  2003. Relation between protonation constants and titration curves in polyprotic acids: a critical view. J. Phys. Chem. B 107:1263–71 [Google Scholar]
  70. Ullmann RT, Ullmann GM. 70.  2012. GMCT: a Monte Carlo simulation package for macromolecular receptors. J. Comp. Chem. 33:887–900 [Google Scholar]
  71. Vila JA. 71.  2012. Limiting values of the 15N chemical shift of the imidazole ring of histidine at high pH. J. Phys. Chem. 116:6665–69 [Google Scholar]
  72. Vila JA, Arnautova YA, Vorobjev Y, Scheraga HA. 72.  2011. Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH. PNAS 108:5602–7 [Google Scholar]
  73. Warshel A, Aqvist J. 73.  1991. Electrostatic energy and macromolecular function. Annu. Rev. Biophys. Biophys. Chem. 20:267–98 [Google Scholar]
  74. Webb H, Tynan-Connolly BM, Gregory ML, Farrell D, O'Meara F. 74.  et al. 2011. Remeasuring HEWL pKa values by NMR spectroscopy: methods, analysis, accuracy, and implications for theoretical pKa calculations. Proteins 79:685–702 [Google Scholar]
  75. Werbeck ND, Kirkpatrick J, Hansen DF. 75.  2013. Probing arginine side-chains and their dynamics with carbon-detected NMR spectroscopy: application to the 42 kDa human histone deacetylase 8 at high pH. Angew. Chem. Int. Ed. Engl. 52:3145–47 [Google Scholar]
  76. Wishart DS, Case DA. 76.  2001. Use of chemical shift in molecular structure determination. Methods Enzymol. 338:3–34 [Google Scholar]
  77. Yamazaki T, Pascal SM, Singer AU, Forman-Kay JD, Kay LE. 77.  1995. NMR pulse sequences for the sequence-specific assignment of arginine guanidino 15N and 1H chemical shifts in proteins. J. Am. Chem. Soc. 117:3556–64 [Google Scholar]
  78. Zhu L, Kemple MD, Yuan P, Prendergast FG. 78.  1995. N-terminus and lysine side chain pKa values of melittin in aqueous solutions and micellar dispersions measured by 15N NMR. Biochemistry 34:13196–202 [Google Scholar]
/content/journals/10.1146/annurev-biophys-083012-130351
Loading
/content/journals/10.1146/annurev-biophys-083012-130351
Loading

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error