Proton nuclear magnetic resonance study of histidine ionizations in myoglobins of various species. Comparison of observed and computed pK values

Botelho, L; Friend, Stephen H.; Matthew, James B.; Lehman, Lee D.; Hanania, G. I. H.; Gurd, Frank R. N.

doi:10.1021/bi00617a020

Cited by 60 publications

(30 citation statements)

References 55 publications

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“…Exceptions at various levels of structural detail have been clearly identified, however. For example, a salt bridge observed by NMR and chemical studies in solution is absent from the myoglobin crystal structure (24). A further assumption often made is that a calculated quantity derived from analysis of a single average structure is equal to the average calculated for a whole ensemble of thermodynamically accessible structures.…”

Section: Resultsmentioning

confidence: 99%

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Northrup

Wensel

Meares

et al. 1990

Proc. Natl. Acad. Sci. U.S.A.

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Energy transfer in the "rapid diffusion" limit from electronically excited terbium(llI) chelates in three different charge states to horse heart ferricytochrome c was measured as a function of ionic strength. Theoretical rate constants calculated by numerical integration of the Forster integral (containing the Poisson-Boltzmann-generated protein electrostatic potential) were compared with the experimental data to evaluate the accuracy of protein electrostatic field calculations at the protein/solvent interface. Two dielectric formalisms were used: a simple coulombic/Debye-Huckel procedure and a finite difference method [Warwicker, J. & Watson, H. C. (1982)J. Mol. Biol. 157, 671-679] that accounts for the low-dielectric protein interior and the irregular protein/solvent boundary. Good agreement with experiment was obtained and the ionic-strength dependence of the reaction was successfully reproduced. The sensitivity of theoretical rate constants to the choices of effective donor sphere size and the energy transfer distance criterion was analyzed. Electrostatic potential and rate-constant calculations were carried out on sets of structures collected along two molecular dynamics trajectories of cytochrome c. Protein conformational fluctuations were shown to produce large variations in the calculated energy transfer-rate constant. We conclude that protein fluctuations and the resulting transient structures can play significant roles in biological or catalytic activities that are not apparent from examination of a static structure. For calculating protein electrostatics, large-scale low-frequency conformational fluctuations, such as charged side-chain reorientation, are established to be as important as the computational method for incorporating dielectric boundary effects.Electrostatic interactions are known to play a significant role in the biological activity of proteins, as indicated by the pH and ionic-strength dependence of virtually all protein reactions (1). Numerous studies have shown that reaction rates between proteins and charged substrates often depend strongly on the solution ionic strength. These observations have been taken to suggest that intermolecular electrostatic forces are important in facilitating the association of reaction complexes. To analyze specific interactions at the molecular level an accurate description of the electrostatic forces around the protein is essential. The electrostatic analysis of proteins by theoretical frameworks is usually couched in terms of the net charge and the dipole moment (2, 3), higher moments (4), or the full asymmetric charge distribution of a single structure derived by crystallography (5-10). One of the more rigorous approaches to the computation of the electrostatic field surrounding proteins in aqueous electrolyte solution involves the iteration of the Poisson-Boltzmann equation by the Warwicker-Watson (WW) algorithm (11). Starting with the protein crystal structure, this procedure accounts for (i) the irregular topography of the protein surfac...

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Section: Resultsmentioning

confidence: 99%

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Northrup

Wensel

Meares

et al. 1990

Proc. Natl. Acad. Sci. U.S.A.

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“…They not only are related to the function of the protein, but also serve as a basis to model electrostatic interactions in proteins (26)(27)(28)(29)(30). Neutron crystallography can directly determine the protonation states of specific histidines (5,19).…”

Section: Discussionmentioning

confidence: 99%

Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin

Shu

Ramakrishnan

Schoenborn

2000

Proc. Natl. Acad. Sci. U.S.A.

116

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Although hydrogens comprise half of the atoms in a protein molecule and are of great importance chemically and structurally, direct visualization of them by using crystallography is difficult. Neutron crystallography is capable of directly revealing the position of hydrogens, but its use on unlabeled samples faces certain technical difficulties: the large incoherent scattering of hydrogen results in background scattering that greatly reduces the signal to noise of the experiment. Moreover, whereas the scattering lengths of C, N, and O are positive, that of hydrogen is negative and about half the magnitude. This results in density for hydrogens being half as strong and close to the threshold of detection at 2.0-Å resolution. Also, because of its opposite sign, there is a partial cancellation of the hydrogen density with that from neighboring atoms, which can lead to ambiguities in interpretation at medium resolution. These difficulties can be overcome by the use of deuterated protein, and we present here a neutron structure of fully deuterated myoglobin. The structure reveals a wealth of chemical information about the molecule, including the geometry of hydrogen bonding, states of protonation of histidines, and the location and geometry of water molecules at the surface of the protein. The structure also should be of broader interest because it will serve as a benchmark for molecular dynamics and energy minimization calculations and for comparison with NMR studies.

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“…The fraction of the surface of the charged site that faces the interior of the protein is then given approximately by the solvent-exposed area in a model peptide less the exposed area in the protein divided by the exposed area in the peptide form, equivalent to (1-SA). The (1-SA) value for each charged Dr. Rothgeb's present address is Department of Chemistry, University of Illinois, Urbana, Ill. 61801 site in the crystallographic protein structure can be used to compute (3,(8)(9)(10)(11) a modulated value for the interaction energy W'ij=Wij(I-SA). (1) Matthew et al (8) showed that a direct adjustment of the effective dielectric constant applying to each pair of charged sites in place of the weighting factor, (1-SA), gave comparable results.…”

Section: Introductionmentioning

confidence: 99%

“…The effective pK at a given pH for the ith site is determined by first assigning to all groups the charge occupancy prescribed by their given intrinsic pK value, pKi", Values of pKint were chosen from the results for small peptides and other model compounds (3,(8)(9)(10), with consideration given to solvent accessibility and hydrogen bonding as previously described (9)(10)(11). Following this initial assignment, an iterative procedure is used for adjusting the various charge loci to the occupancy of all others according to their respective Wij values until equilibrium is reached (1,3,(8)(9)(10). The pK for the ith site can be expressed as…”

Section: Introductionmentioning

confidence: 99%

Electrostatic stabilization in sperm whale and harbor seal myoglobins. Identification of groups primarily responsible for changes in anchoring of the A helix

Gurd¹,

Friend²,

Rothgeb³

et al. 1980

Biophysical Journal

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The compact, largely helical structure of sperm whale and harbor seal myoglobins undergoes an abrupt one-step transition between pH 4.5 and 3.5 as monitored by changes in either the heme Soret band absorbance or circular dichroism probes of secondary structure, for which a modified Tanford-Kirkwood theory provides identification of certain dominant electrostatic interactions responsible for the loss of stability. A similar treatment permits identification of the electrostatic interactions primarily responsible for a process in which the anchoring of the A helix to other parts of the molecule is weakened. This process is detected with both myoglobins, in a pH range approximately 1 unit higher than the onset of the overall unfolding process, through changes in the circular dichroic spectra near 295 nm which correspond to the L1 O-O band of the only two tryptophan residues in these proteins, residues 7 and 14. In each case protonation of certain sites in neighboring parts of the molecule can be identified as producing destabilizing interactions with components of the A helix, particularly with lysine 6.

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Proton nuclear magnetic resonance study of histidine ionizations in myoglobins of various species. Comparison of observed and computed pK values

Cited by 60 publications

References 55 publications

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Electrostatic field around cytochrome c: theory and energy transfer experiment.

Enhanced visibility of hydrogen atoms by neutron crystallography on fully deuterated myoglobin

Electrostatic stabilization in sperm whale and harbor seal myoglobins. Identification of groups primarily responsible for changes in anchoring of the A helix

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