High-Precision Measurement of Hydrogen Bond Lengths in Proteins by Nuclear Magnetic Resonance Methods

Harris, Thomas K.; Mildvan, Albert S.

doi:10.1002/(sici)1097-0134(19990515)35:3<275::aid-prot1>3.0.co;2-v

Cited by 163 publications

(201 citation statements)

References 49 publications

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“…below) between Glu-204/Glu-194 side chains in high-resolution X-ray structures for both the bR ground state and the L state is consistent with the idea of trapping a proton between these 2 residues (15, 16); considering the uncertainty in hydrogenbonding distances even in high-resolution X-ray structures (17), however, the structural data alone do not provide a conclusive statement.…”

supporting

confidence: 74%

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Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

Phatak

Ghosh

et al. 2008

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

135

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The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally difficult to determine unambiguously. Using combined quantum mechanical/ molecular mechanical computations, we demonstrate that a pair of conserved glutamate residues (Glu 194/204) bonded by a delocalized proton is the proton release group that has been long sought in the proton pump, bacteriorhodopsin. This model is consistent with all available experimental structural and infrared data for both the wild-type bacteriorhodopsin and several mutants. In particular, the continuum infrared band in the 1,800-to 2,000-cm ؊1 region is shown to arise due to the partially delocalized nature of the proton between the glutamates in the wild-type bacteriorhodopsin; alternations in the flexibility of the glutamates and electrostatic nature of nearby residues in various mutants modulate the degree of proton delocalization and therefore intensity of the continuum band. The strong hydrogen bond between Glu 194/204 also significantly shifts the carboxylate stretches of these residues well <1,700 cm ؊1 , which explains why carboxylate spectral shift was not observed experimentally in the typical >1,700-cm ؊1 region upon proton release. By contrast, simulations with the proton restrained on the nearby water cluster, as proposed by several recent studies [see, for example, Garezarek K, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109], led to significant structural deviations from available X-ray structures. This study establishes a biological function for strong, low-barrier hydrogen bonds.infrared spectroscopy ͉ proton pumping ͉ water cluster ͉ quantum mechanical/molecular mechanical simulations

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confidence: 74%

“…2F to Table 1). These changes are much larger than the expected uncertainties in the X-ray structures at the respective resolution (17), which strongly indicates that the protonated water cluster model is unlikely to reflect reality.…”

Section: Results and Discussion Structural Features Of Wt Br X-ray Crmentioning

confidence: 99%

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

Phatak

Ghosh

et al. 2008

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

135

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“…1D 1 H, 2D 1 H-1 H NOESY, and 2D 1 H-15 N HSQC spectra were acquired using previously reported methods (29,43). Hydrogen bond distances were estimated from NMR chemical shifts using published correlations that relate the measured chemical shift of the hydrogen-bonded proton to the O⅐⅐⅐O or H⅐⅐⅐O-acceptor distances (26,42). Spectral deconvolutions were carried out using the ACD/NMR Processor software.…”

Section: Methodsmentioning

confidence: 99%

“…These distance changes are estimated to be 0.06 Å based on the observed chemical shift differences (26). A change in proton position of this magnitude is expected to be accompanied by a lengthening of the hydrogen bond O⅐⅐⅐O distances by approximately 0.04 Å (22,42). Thus, lengthening of the Tyr-42 and Glu-46 hydrogen bonds upon charge delocalization from the chromophore oxygen appears to be an intrinsic property of these interactions that will contribute to conformational rearrangements during the PYP photocycle.…”

Section: The Effect Of Chromophore Charge Delocalization On the Strucmentioning

confidence: 99%

Hydrogen bond dynamics in the active site of photoactive yellow protein

Sigala

Tsuchida

Herschlag

2009

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

145

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Hydrogen bonds play major roles in biological structure and function. Nonetheless, hydrogen-bonded protons are not typically observed by X-ray crystallography, and most structural studies provide limited insight into the conformational plasticity of individual hydrogen bonds or the dynamical coupling present within hydrogen bond networks. We report the NMR detection of the hydrogen-bonded protons donated by Tyr-42 and Glu-46 to the chromophore oxygen in the active site of the bacterial photoreceptor, photoactive yellow protein (PYP). We have used the NMR resonances for these hydrogen bonds to probe their conformational properties and ability to rearrange in response to nearby electronic perturbation. The detection of geometric isotope effects transmitted between the Tyr-42 and Glu-46 hydrogen bonds provides strong evidence for robust coupling of their equilibrium conformations. Incorporation of a modified chromophore containing an electron-withdrawing cyano group to delocalize negative charge from the chromophore oxygen, analogous to the electronic rearrangement detected upon photon absorption, results in a lengthening of the Tyr-42 and Glu-46 hydrogen bonds and an attenuated hydrogen bond coupling. The results herein elucidate fundamental properties of hydrogen bonds within the complex environment of a protein interior. Furthermore, the robust conformational coupling and plasticity of hydrogen bonds observed in the PYP active site may facilitate the larger-scale dynamical coupling and signal transduction inherent to the biological function that PYP has evolved to carry out and may provide a model for other coupled dynamic systems.charge delocalization ͉ hydrogen bond coupling ͉ protein structure ͉ signal transduction

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“…Thus, the >2-unit decrease in the pK a of His-95 must result from both the electrostatic and hydrogen bond contributions by the N-terminus of the α-helix. The use of neutral His-95 as an electrophilic catalyst can be rationalized in that the enzyme may have evolved to match the pK a for ionization of neutral His-95 to its conjugate imidazolate anion base with the pK a of the intermediate enediol(ate), facilitating the formation of a short, strong hydrogen bond (43,44).…”

Section: N-terminus Of a α-Helixmentioning

confidence: 99%

Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites

2002

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SummaryIn protein and RNA macromolecules, only a limited number of different side-chain chemical groups are available to function as catalysts. The myriad of enzyme-catalyzed reactions results from the ability of most of these groups to function either as nucleophilic, electrophilic, or general acid-base catalysts, and the key to their adapted chemical function lies in their states of protonation. Ionization is determined by the intrinsic pK a of the group and the microenvironment created around the group by the protein or RNA structure, which perturbs its intrinsic pK a to its functional or apparent pK a . These pK a shifts result from interactions of the catalytic group with other fully or partially charged groups as well as the polarity or dielectric of the medium that surrounds it. The electro- Abbreviations: AAD, acetoacetate decarboxylase; AbAld, antibody aldolase; Ala-Race, alanine racemase; hdvAR, hepatitis delta virus antigenomic ribozyme; ArsC, arsenate reductase; AspAT, aspartate aminotransferase; BCX, Bacillus circulans xylanase; BR, ground-state bacteriorhodopsin with all trans retinal, protonated D96, protonated Schiff base, and unprotonated D85; BR-M, excited M-state bacteriorhodopsin with 13-cis retinal, protonated D96, unprotonated Schiff base, and protonated D85; BR-N, excited N-state bacteriorhodopsin with 13-cis retinal, unprotonated D96, protonated Schiff base, and protonated D85; Chy-TFKs, chymotrypsin complexed with various peptidyl trifluoroketones; hmCK, human muscle creatine kinase; DsbA and DsbC, disulfide bond enzymes A and C in E. coli; GalE, UDP-galactose 4-epimerase; GRX, glutaredoxin; HB, hydrogen bond; HPE, hydrophobic environment; KSI, ketosteroid isomerase; LBHB, low-barrier hydrogen bond; NMR, nuclear magnetic resonance; NTα, N-terminus of an α-helix; Nuc/Lv, nucleophile/leaving group; 4-OT, 4-oxalocrotonate tautomerase; PDI, protein disulfide isomerase; PLP, pyridoxal 5 -phosphate; PMP, pyridoxamine 5 -phosphate; blmPTP, bovine liver low molecular weight protein tyrosine phosphatase; hPTP1, human protein tyrosine phosphatase; yPTP, Yersenia protein tyrosine phosphatase; rPTC, ribosomal peptidyl transferase center; RNaseH1, ribonuclease H1; TIM, triosephosphate isomerase; bTRX, bacterial thioredoxin; hTRX, human thioredoxin.

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High-Precision Measurement of Hydrogen Bond Lengths in Proteins by Nuclear Magnetic Resonance Methods

Abstract: We have compared hydrogen bond lengths on enzymes derived with high precision (I ؎0 .

Cited by 163 publications

References 49 publications

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin

Hydrogen bond dynamics in the active site of photoactive yellow protein

Structural Basis of Perturbed pKa Values of Catalytic Groups in Enzyme Active Sites

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