Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. The pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A

Markley, John L.

doi:10.1021/bi00687a007

Cited by 62 publications

(64 citation statements)

References 30 publications

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“…There appears to be a considerable discrepancy between the pK' values proposed by both workers for Asp-14 (4.2 and 5.6). Furthermore the pK' of His48 in RNase-A is 6.0 [6], which is different from the value of 6.9 suggested by Markley [37]. Nevertheless there is good evidence from an earlier fast kinetic study [45] for a pH-induced conformational change.…”

Section: H-'h Exchungementioning

confidence: 60%

“…The one that occurs at lower pH also perturbs a tyrosine residue, which has been assigned as Tyr-25. It is suggested that the conformational change centred on pH 5.6 is due to the dissociation of Asp-14 and that centred on pH 6.9 to the dissociation of His-48 [37]. There appears to be a considerable discrepancy between the pK' values proposed by both workers for Asp-14 (4.2 and 5.6).…”

Section: H-'h Exchungementioning

confidence: 91%

“…Such large differences result from the errors inherent in the observation of small 'H NMR resonances which change in area (and height) as a function of time, together with the possibility of the occurrence of broad underlying NH resonances that may vary in area with pH [37]. There can be no doubt that the method is much more accurate when dealing with small model compounds [20,24, and unpublished results], in which case the 'noise' level is minimised and there is no possibility of the occurrence of other small overlapping peaks, that may prevent the obtaining of a correct result.…”

Section: H-2h Exchange Kineticsmentioning

confidence: 99%

“…With RNase-A many workers [15,30,31,37] have observed the fact that in the absence of acetate ions the resonance from histidine-48 occurs at a constant chemical shift below about pH 5.4, but above this pH it rapidly broadens and disappears. Markley [37] has observed the reappearance of the resonance at higher field at pH > 6.1 and given an interpretation of the phenomenon. However the C-2 proton resonance of histidine-48 of S-protein shifts upfield with increase of pH as shown in Fig.…”

Section: Studies On S-protein From Rnase-amentioning

confidence: 99%

“…The effect is supposedly mediated over some distance as a result of a conformational change that affects Asp-14 and His-48 [44]. In another NMR study [37] it has been proposed that the histidine-48 hinge region undergoes two conformational changes with mid points at pH 5.6 and 6.9. The one that occurs at lower pH also perturbs a tyrosine residue, which has been assigned as Tyr-25.…”

Section: H-'h Exchungementioning

confidence: 99%

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Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Bradbury

Crompton

Teh

1977

European Journal of Biochemistry

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1H NMR spectroscopy at 100 MHz was used to determine the first‐order rate constants for the 1H‐2H exchange of the H‐2 histidine resonances of RNase‐A in 2H2O at 35°C and pH meter readings of 7, 9, 10 and 10.5. Prolonged exposure in 2H2O at 35°C and pH meter reading 11 caused irreversible denaturation of RNase‐A. The rate constants at pH 7 and 9 agreed reasonably well with those obtained in 1H‐3H exchange experiments by Ohe, J., Matsuo, H., Sakiyama, F. and Narita, K. [J. Biochem. (Tokyo) 75, 1197–1200 1974)]. The rate data obtained by various authors is summarised and the reasons for the poor agreement between the data is discussed. The first‐order rate constant for the exchange of His‐48 increases rapidly from near zero at pH 9 (due to its inaccessibility to solvent) with increase of pH to 10.5. The corresponding values for His‐119 show a decrease and those for His‐12 a small increase over the same pH range. These changes are attributed to a conformational change in the hinge region of RNase‐A (probably due to the titration of Tyr‐25) which allows His‐48 to become accessible to solvent. 1H NMR spectra of S‐protein and S‐peptide, and of material partially deuterated at the C‐2 positions of the histidine residues confirm the reassignment of the histidine resonances of RNase‐A [Bradbury, J. H. & Teh, J. S. (1975) Chem. Commun., 936–937]. The chemical shifts of the C‐2 and C‐4 protons of histidine‐12 of S‐peptide are followed as a function of pH and a pK′ value of 6.75 is obtained. The reassignment of the three C‐2 histidine resonances of S‐protein is confirmed by partial deuteration studies. The pK′ values obtained from titration of the H‐2 resonances of His‐48, His‐105 and His‐119 are 5.3, 6.5 and 6.0, respectively. The S‐protein is less stable to acid than RNase‐A since the former, but not the latter, shows evidence of reversible denaturation at pH 3 and 26°C. His‐48 in S‐protein titrates normally and has a lower pK than in RNase‐A probably because of the absence of Asp‐14, which in RNase‐A forms a hydrogen bond with His‐48 and causes it to be inaccessible to solvent, at pH values below 9.

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Section: H-'h Exchungementioning

confidence: 60%

Section: H-'h Exchungementioning

confidence: 91%

Section: H-2h Exchange Kineticsmentioning

confidence: 99%

Section: Studies On S-protein From Rnase-amentioning

confidence: 99%

Section: H-'h Exchungementioning

confidence: 99%

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Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Bradbury

Crompton

Teh

1977

European Journal of Biochemistry

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Variability in the pKa of histidine side‐chains correlates with burial within proteins

2002

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Acidic pKas of histidines buried within the protein interior are frequently rationalized on the contradictory basis of either polar interactions within the protein or the effects of a hydrophobic environment. To examine these relationships, we surveyed the buried surface area, depth of burial, polar interactions, and crystallographic temperature factors of histidines of known pKa. It has been found that buried environments of histidines do not always result in acidic pKas. Instead, the variability of histidine pKas increases for residues where the majority of the side-chain is buried. Because buried histidines are always found in mixed polar/apolar environments, multiple environmental contributions to pKa values must be considered. However, the quantitative relationships between heterogeneous environments and pKa values are not immediately apparent from the available data.

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Optimizing pK_A computation in proteins with pH adapted conformations

2007

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pK(A) in proteins are determined by electrostatic energy computations using a small number of optimized protein conformations derived from crystal structures. In these protein conformations hydrogen positions and geometries of salt bridges on the protein surface were determined self-consistently with the protonation pattern at three pHs (low, ambient, and high). Considering salt bridges at protein surfaces is most relevant, since they open at low and high pH. In the absence of these conformational changes, computed pK(A)(comp) of acidic (basic) groups in salt bridges underestimate (overestimate) experimental pK(A)(exp), dramatically. The pK(A)(comp) for 15 different proteins with 185 known pK(A)(exp) yield an RMSD of 1.12, comparable with two other methods. One of these methods is fully empirical with many adjustable parameters. The other is also based on electrostatic energy computations using many non-optimized side chain conformers but employs larger dielectric constants at short distances of charge pairs that diminish their electrostatic interactions. These empirical corrections that account implicitly for additional conformational flexibility were needed to describe the energetics of salt bridges appropriately. This is not needed in the present approach. The RMSD of the present approach improves if one considers only strongly shifted pK(A)(exp) in contrast to the other methods under these conditions. Our method allows interpreting pK(A)(comp) in terms of pH dependent hydrogen bonding pattern and salt bridge geometries. A web service is provided to perform pK(A) computations.

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Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. The pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A

Abstract: Abbreviations used are: RNase, bovine pancreatic ribonuclease; pH*, uncorrected pH meter reading of a D2O solution made with a glass electrode standardized in H2O buffers; 3'-CMP, cytidine 3'-monophosphate.

Cited by 62 publications

References 30 publications

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Variability in the pKa of histidine side‐chains correlates with burial within proteins

Optimizing pK_A computation in proteins with pH adapted conformations

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Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. The pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A

Abstract: Abbreviations used are: RNase, bovine pancreatic ribonuclease; pH*, uncorrected pH meter reading of a D2O solution made with a glass electrode standardized in H2O buffers; 3'-CMP, cytidine 3'-monophosphate.

Cited by 62 publications

References 30 publications

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of 1H‐2H Exchange of Ribonuclease A

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of 1H‐2H Exchange of Ribonuclease A

Variability in the pKa of histidine side‐chains correlates with burial within proteins

Optimizing pKA computation in proteins with pH adapted conformations

Contact Info

Product

Resources

About

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Nuclear‐Magnetic‐Resonance Study of the Histidine Residues of S‐Peptide and S‐Protein and Kinetics of ¹H‐²H Exchange of Ribonuclease A

Optimizing pK_A computation in proteins with pH adapted conformations